### broadBernstein.txt wrangler notes for all submissions

select id,name,status from projects where name like "Broad%";
+-----+--------------------------------------------+------------+
| id  | name                                       | status     |
+-----+--------------------------------------------+------------+
|  66 | Broad ChIPSeq K562 112008                  | superceded |
| 108 | Broad Raw Signal Regeneration              | superceded |
| 140 | Broad ChIPSeq GM12878 H3K4me3 010409       | released   |
| 141 | Broad ChIPSeq GM12878 H3K4me2 010408       | released   |
| 142 | Broad ChIPSeq GM12878 H3K4me1 010408       | released   |
| 143 | Broad ChIPSeq GM12878 H3K36me3 010408      | released   |
| 144 | Broad ChIPSeq GM12878 H3K27me3 010408      | released   |
| 145 | Broad ChIPSeq GM12878 H3K27ac 010408       | released   |
| 146 | Broad ChIPSeq GM12878 H3K9ac 010408        | released   |
| 147 | Broad ChIPSeq GM12878 H4K20me1 010409      | released   |
| 148 | Broad ChIPSeq GM12878 CTCF 010409          | released   |
| 149 | Broad ChIPSeq GM12878 WCE 010409           | released   |
| 150 | Broad ChIPSeq K562 H3K4me3 010409          | released   |
| 151 | Broad ChIPSeq K562 H3K4me2 010409          | released   |
| 152 | Broad ChIPSeq K562 H3K4me1 010409          | released   |
| 153 | Broad ChIPSeq K562 H3K27me3 010409         | released   |
| 154 | Broad ChIPSeq K562 H3K36me3 010409         | released   |
| 155 | Broad ChIPSeq K562 H3K9ac 010409           | released   |
| 156 | Broad ChIPSeq K562 H3K27ac 010409          | released   |
| 157 | Broad ChIPSeq K562 CTCF 010409             | released   |
| 158 | Broad ChIPSeq K562 H3K9me1 010409          | released   |
| 159 | Broad ChIPSeq K562 H4K20me1 010409         | released   |
| 160 | Broad ChIPSeq K562 Pol2 010409             | released   |
| 161 | Broad ChIPSeq K562 WCE 010409              | released   |
| 162 | Broad ChIPSeq HUVEC H3K4me3 010409         | released   |
| 163 | Broad ChIPSeq HUVEC H3K4me2 010409         | released   |
| 164 | Broad ChIPSeq HUVEC H3K4me1 010409         | released   |
| 165 | Broad ChIPSeq HUVEC H3K27me3 010409        | released   |
| 166 | Broad ChIPSeq HUVEC H3K36me3 010409        | released   |
| 167 | Broad ChIPSeq HUVEC H3K9ac 010409          | released   |
| 168 | Broad ChIPSeq HUVEC H3K27ac 010409         | released   |
| 169 | Broad ChIPSeq HUVEC H3K9me1 010409         | released   |
| 170 | Broad ChIPSeq HUVEC H4K20me1 010409        | released   |
| 171 | Broad ChIPSeq HUVEC CTCF 010409            | released   |
| 172 | Broad ChIPSeq HUVEC Pol2 010409            | released   |
| 173 | Broad ChIPSeq HUVEC WCE 010409             | released   |
| 174 | Broad ChIPSeq Keratinocyte H3K4me3 010409  | released   |
| 175 | Broad ChIPSeq Keratinocyte H3K4me2 010409  | released   |
| 176 | Broad ChIPSeq Keratinocyte H3K4me1 010409  | released   |
| 177 | Broad ChIPSeq Keratinocyte H3K27me3 010409 | released   |
| 178 | Broad ChIPSeq Keratinocyte H3K36me3 010409 | released   |
| 179 | Broad ChIPSeq Keratinocyte H3K9ac 010409   | released   |
| 180 | Broad ChIPSeq Keratinocyte H3K27ac 010409  | released   |
| 181 | Broad ChIPSeq Keratinocyte H3K9me1         | released   |
| 182 | Broad ChIPSeq Keratinocyte H4K20me1 010409 | released   |
| 183 | Broad ChIPSeq Keratinocyte CTCF 010409     | released   |
| 184 | Broad ChIPSeq Keratinocyte Pol2 010409     | released   |
| 185 | Broad ChIPSeq Keratinocyte WCE 010409      | released   |
+-----+--------------------------------------------+------------+
48 rows in set (0.00 sec)

Broad 11-20
===========
1) cd 66;mv ../../ftp/prod/tarjei/Broad* .
2) tar -xzf Broad*.tgz
  tar -xzf BroadChipSeq_K562_H3K27ac_111908.tgz 
  mv BroadChipSeq_K562_H3K27ac_111908.tgz 001_BroadChipSeq_K562_H3K27ac_111908.tgz
  tar;mv;tar;mv ...
Everything expands to seq/tarjeiscratch/ENCODE/K562/data/ instead of data/
  mv seq/tarjeiscratch/ENCODE/K562/data .
3) Validate
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1
	File 'data/Broad_Raw_K562_H3K4me3_rep1_chr*.fastq' does not exist (possibly bad glob?)
		Fix DDF
	Invalid tagAlign file; line 1 in file 'data/Broad_Raw_K562_H3K4me3_rep1_chr1.bed' is invalid:
	line: chr1      236781326       236781378       SL-XBE_3_FC30CLLAAXX:6:7:148:1114       GACAATTTATGGAGAAATATTAATCACAGTGCCTCATTAATTAATTCATTT      1000    + [validateTagAlign]
	chr1      236781326       236781378       SL-XBE_3_FC30CLLAAXX:6:7:148:1114       GACAATTTATGGAGAAATATTAATCACAGTGCCTCATTAATTAATTCATTT      1000    +
	mv Broad_Raw_K562_WCE_rep2_chrX.bed old
    	awk '{printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$5,$6,$7;}' Broad_Raw_K562_WCE_rep2_chrX.bed > Broad_Raw_K562_WCE_rep2_chrX.bed.test
  cd data
  mkdir old
  mv *.bed old/
  cd old
  for file in *.bed
    do
    echo Fixing $file...
    awk '{printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$5,$6,$7;}' $file > ../$file
  done
	
	File 'data/Broad_K562_H3K4me3_chr1.wig' failed wiggle validation: Found start=0 at line 1, the first chrom position is 1, not 0
  cd data
  mkdir old
  mv *.wig old/
  cd old
  for file in *.wig
    do
    echo Fixing $file...
    cat $file | sed s/"start=0"/"start=1"/g > ../$file
  done

		cd data	
		grep fixedStep Broad_K562_H3K4me3_chr1.wig
		grep -v fixedStep Broad_K562_H3K4me3_chr1.wig > new/Broad_K562_H3K4me3_chr1.wig

Broad 11-26
===========
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1 &
Failed..
Added medianFragmentLength 225
removed controls
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/66 > upload_error 2>&1 &

Broad 11-30 Control
===================
edit BroadChipSeq.ddf to BroadChipSeqJustInput.DDF
alter doEncodeValidate.pl to ignore required on control or input.
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/66 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/66 > upload_error 2>&1 &

| wgEncodeBroadChipSeqRawSignalRep1K562Control  |
| wgEncodeBroadChipSeqRawSignalRep1K562Ctcf     |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k27ac  |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k27me3 |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k36me3 |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k4me1  |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k4me2  |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k4me3  |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k9ac   |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k9me1  |
| wgEncodeBroadChipSeqRawSignalRep1K562H4k20me1 |
| wgEncodeBroadChipSeqRawSignalRep1K562Pol2b    |
| wgEncodeBroadChipSeqRawSignalRep2K562Control  |
| wgEncodeBroadChipSeqRawSignalRep2K562Ctcf     |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k27ac  |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k27me3 |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k36me3 |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k4me1  |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k4me2  |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k4me3  |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k9ac   |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k9me1  |
| wgEncodeBroadChipSeqRawSignalRep2K562H4k20me1 |
| wgEncodeBroadChipSeqRawSignalRep2K562Pol2b    |

data/Broad_Raw_K562_H3K4me3_rep1_chr*.bed       Alignments      K562    H3K4me3                 1
data/Broad_Raw_K562_H3K4me3_rep2_chr*.bed       Alignments      K562    H3K4me3                 2
data/Broad_Raw_K562_H3K4me2_rep1_chr*.bed       Alignments      K562    H3K4me2                 1
data/Broad_Raw_K562_H3K4me2_rep2_chr*.bed       Alignments      K562    H3K4me2                 2
data/Broad_Raw_K562_H3K4me1_rep1_chr*.bed       Alignments      K562    H3K4me1                 1
data/Broad_Raw_K562_H3K4me1_rep2_chr*.bed       Alignments      K562    H3K4me1                 2
data/Broad_Raw_K562_H3K9ac_rep1_chr*.bed        Alignments      K562    H3K9ac                  1
data/Broad_Raw_K562_H3K9ac_rep2_chr*.bed        Alignments      K562    H3K9ac                  2
data/Broad_Raw_K562_H3K27ac_rep1_chr*.bed       Alignments      K562    H3K27ac                 1
data/Broad_Raw_K562_H3K27ac_rep2_chr*.bed       Alignments      K562    H3K27ac                 2
data/Broad_Raw_K562_H3K27me3_rep1_chr*.bed      Alignments      K562    H3K27me3                        1
data/Broad_Raw_K562_H3K27me3_rep2_chr*.bed      Alignments      K562    H3K27me3                        2
data/Broad_Raw_K562_H3K36me3_rep1_chr*.bed      Alignments      K562    H3K36me3                        1
data/Broad_Raw_K562_H3K36me3_rep2_chr*.bed      Alignments      K562    H3K36me3                        2
data/Broad_Raw_K562_H3K9me1_rep1_chr*.bed       Alignments      K562    H3K9me1                 1
data/Broad_Raw_K562_H3K9me1_rep2_chr*.bed       Alignments      K562    H3K9me1                 2
data/Broad_Raw_K562_H4K20me1_rep1_chr*.bed      Alignments      K562    H4K20me1                        1
data/Broad_Raw_K562_H4K20me1_rep2_chr*.bed      Alignments      K562    H4K20me1                        2
data/Broad_Raw_K562_CTCF_rep1_chr*.bed  Alignments      K562    CTCF                    1
data/Broad_Raw_K562_CTCF_rep2_chr*.bed  Alignments      K562    CTCF                    2
data/Broad_Raw_K562_Pol2_rep1_chr*.bed  Alignments      K562    Pol2(b)                 1
data/Broad_Raw_K562_Pol2_rep2_chr*.bed  Alignments      K562    Pol2(b)                 2
data/Broad_Raw_K562_WCE_rep1_chr*.bed   Alignments      K562    Control                 1
data/Broad_Raw_K562_WCE_rep2_chr*.bed   Alignments      K562    Control                 2

mkdir data
cp ../66/data/Broad_Raw_K562_H3K4me3_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K4me3_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K4me2_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K4me2_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K4me1_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K4me1_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K9ac_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K9ac_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K27ac_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K27ac_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K27me3_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K27me3_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K36me3_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K36me3_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K9me1_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H3K9me1_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H4K20me1_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_H4K20me1_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_CTCF_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_CTCF_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_Pol2_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_Pol2_rep2_chr*.bed data/
cp ../66/data/Broad_Raw_K562_WCE_rep1_chr*.bed data/
cp ../66/data/Broad_Raw_K562_WCE_rep2_chr*.bed data/

head -1 ../66/BroadChipSeq.DDF > BroadChipSeq.DDF
grep Alignment ../66/BroadChipSeq.DDF >> BroadChipSeq.DDF
cp ../66/BroadChipSeq.DAF > BroadChipSeq.DAF
edit
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/108 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/108 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/108 > upload_error 2>&1 &


Peaks in downloads dir
====================
|  66 | Broad ChIPSeq K562 112008               | displayed       |
cd 66
data/Broad_K562_CTCF_chr*.pk    Peaks   K562    CTCF            080608
data/Broad_K562_H3K27ac_chr*.pk Peaks   K562    H3K27ac         080608
data/Broad_K562_H3K27me3_chr*.pk        Peaks   K562    H3K27me3                080608
data/Broad_K562_H3K36me3_chr*.pk        Peaks   K562    H3K36me3                080608
data/Broad_K562_H3K4me1_chr*.pk Peaks   K562    H3K4me1         080608
data/Broad_K562_H3K4me2_chr*.pk Peaks   K562    H3K4me2         080608
data/Broad_K562_H3K4me3_chr*.pk Peaks   K562    H3K4me3         080608
data/Broad_K562_H3K9ac_chr*.pk  Peaks   K562    H3K9ac          080608
data/Broad_K562_H3K9me1_chr*.pk Peaks   K562    H3K9me1         080608
data/Broad_K562_H4K20me1_chr*.pk        Peaks   K562    H4K20me1                080608
data/Broad_K562_Pol2_chr*.pk    Peaks   K562    Pol2(b)         080608
 rm tmp.pk
 touch tmp.pk
 for F in data/Broad_K562_Pol2_chr*.pk
 do
   ll $F
   cat $F >> tmp.pk
 done
 ll tmp.pk

/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562Ctcf.broadPeak.gz &                
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k27ac.broadPeak.gz &             
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k27me3.broadPeak.gz &            
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k36me3.broadPeak.gz &            
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k4me1.broadPeak.gz &             
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k4me2.broadPeak.gz &             
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k4me3.broadPeak.gz &             
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k9ac.broadPeak.gz &              
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H3k9me1.broadPeak.gz &             
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562H4k20me1.broadPeak.gz &            
/bin/gzip -c tmp.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksK562Pol2b.broadPeak.gz &               

Broad Again 2009-01-05
======================
| wgEncodeBroadChipSeqPeaksK562Ctcf             |
| wgEncodeBroadChipSeqPeaksK562H3k27ac          |
| wgEncodeBroadChipSeqPeaksK562H3k27me3         |
| wgEncodeBroadChipSeqPeaksK562H3k36me3         |
| wgEncodeBroadChipSeqPeaksK562H3k4me1          |
| wgEncodeBroadChipSeqPeaksK562H3k4me2          |
| wgEncodeBroadChipSeqPeaksK562H3k4me3          |
| wgEncodeBroadChipSeqPeaksK562H3k9ac           |
| wgEncodeBroadChipSeqPeaksK562H3k9me1          |
| wgEncodeBroadChipSeqPeaksK562H4k20me1         |
| wgEncodeBroadChipSeqPeaksK562Pol2b            |
| wgEncodeBroadChipSeqRawSignalRep1K562Control  |
| wgEncodeBroadChipSeqRawSignalRep1K562Ctcf     |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k27ac  |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k27me3 |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k36me3 |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k4me1  |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k4me2  |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k4me3  |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k9ac   |
| wgEncodeBroadChipSeqRawSignalRep1K562H3k9me1  |
| wgEncodeBroadChipSeqRawSignalRep1K562H4k20me1 |
| wgEncodeBroadChipSeqRawSignalRep1K562Pol2b    |
| wgEncodeBroadChipSeqRawSignalRep2K562Control  |
| wgEncodeBroadChipSeqRawSignalRep2K562Ctcf     |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k27ac  |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k27me3 |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k36me3 |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k4me1  |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k4me2  |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k4me3  |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k9ac   |
| wgEncodeBroadChipSeqRawSignalRep2K562H3k9me1  |
| wgEncodeBroadChipSeqRawSignalRep2K562H4k20me1 |
| wgEncodeBroadChipSeqRawSignalRep2K562Pol2b    |
| wgEncodeBroadChipSeqSignalK562Ctcf            |
| wgEncodeBroadChipSeqSignalK562H3k27ac         |
| wgEncodeBroadChipSeqSignalK562H3k27me3        |
| wgEncodeBroadChipSeqSignalK562H3k36me3        |
| wgEncodeBroadChipSeqSignalK562H3k4me1         |
| wgEncodeBroadChipSeqSignalK562H3k4me2         |
| wgEncodeBroadChipSeqSignalK562H3k4me3         |
| wgEncodeBroadChipSeqSignalK562H3k9ac          |
| wgEncodeBroadChipSeqSignalK562H3k9me1         |
| wgEncodeBroadChipSeqSignalK562H4k20me1        |
| wgEncodeBroadChipSeqSignalK562Pol2b           |

#rename table wgEncodeBroadChipSeqRawSignalRep1K562Control  to sav_wgEncodeBroadChipSeqRawSignalRep1K562Control ;
#rename table wgEncodeBroadChipSeqRawSignalRep2K562Control  to sav_wgEncodeBroadChipSeqRawSignalRep2K562Control ;

rename table wgEncodeBroadChipSeqPeaksK562Ctcf             to sav_wgEncodeBroadChipSeqPeaksK562Ctcf;
rename table wgEncodeBroadChipSeqPeaksK562H3k27ac          to sav_wgEncodeBroadChipSeqPeaksK562H3k27ac         ;
rename table wgEncodeBroadChipSeqPeaksK562H3k27me3         to sav_wgEncodeBroadChipSeqPeaksK562H3k27me3        ;
rename table wgEncodeBroadChipSeqPeaksK562H3k36me3         to sav_wgEncodeBroadChipSeqPeaksK562H3k36me3        ;
rename table wgEncodeBroadChipSeqPeaksK562H3k4me1          to sav_wgEncodeBroadChipSeqPeaksK562H3k4me1         ;
rename table wgEncodeBroadChipSeqPeaksK562H3k4me2          to sav_wgEncodeBroadChipSeqPeaksK562H3k4me2         ;
rename table wgEncodeBroadChipSeqPeaksK562H3k4me3          to sav_wgEncodeBroadChipSeqPeaksK562H3k4me3         ;
rename table wgEncodeBroadChipSeqPeaksK562H3k9ac           to sav_wgEncodeBroadChipSeqPeaksK562H3k9ac          ;
rename table wgEncodeBroadChipSeqPeaksK562H3k9me1          to sav_wgEncodeBroadChipSeqPeaksK562H3k9me1         ;
rename table wgEncodeBroadChipSeqPeaksK562H4k20me1         to sav_wgEncodeBroadChipSeqPeaksK562H4k20me1        ;
rename table wgEncodeBroadChipSeqPeaksK562Pol2b            to sav_wgEncodeBroadChipSeqPeaksK562Pol2b           ;
rename table wgEncodeBroadChipSeqRawSignalRep1K562Ctcf     to sav_wgEncodeBroadChipSeqRawSignalRep1K562Ctcf    ;
rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k27ac  to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k27ac ;
rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k27me3 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k27me3;
rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k36me3 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k36me3;
rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k4me1  to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k4me1 ;
rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k4me2  to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k4me2 ;
rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k4me3  to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k4me3 ;
rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k9ac   to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k9ac  ;
rename table wgEncodeBroadChipSeqRawSignalRep1K562H3k9me1  to sav_wgEncodeBroadChipSeqRawSignalRep1K562H3k9me1 ;
rename table wgEncodeBroadChipSeqRawSignalRep1K562H4k20me1 to sav_wgEncodeBroadChipSeqRawSignalRep1K562H4k20me1;
rename table wgEncodeBroadChipSeqRawSignalRep1K562Pol2b    to sav_wgEncodeBroadChipSeqRawSignalRep1K562Pol2b   ;
rename table wgEncodeBroadChipSeqRawSignalRep2K562Ctcf     to sav_wgEncodeBroadChipSeqRawSignalRep2K562Ctcf    ;
rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k27ac  to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k27ac ;
rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k27me3 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k27me3;
rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k36me3 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k36me3;
rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k4me1  to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k4me1 ;
rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k4me2  to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k4me2 ;
rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k4me3  to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k4me3 ;
rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k9ac   to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k9ac  ;
rename table wgEncodeBroadChipSeqRawSignalRep2K562H3k9me1  to sav_wgEncodeBroadChipSeqRawSignalRep2K562H3k9me1 ;
rename table wgEncodeBroadChipSeqRawSignalRep2K562H4k20me1 to sav_wgEncodeBroadChipSeqRawSignalRep2K562H4k20me1;
rename table wgEncodeBroadChipSeqRawSignalRep2K562Pol2b    to sav_wgEncodeBroadChipSeqRawSignalRep2K562Pol2b   ;
rename table wgEncodeBroadChipSeqSignalK562Ctcf            to sav_wgEncodeBroadChipSeqSignalK562Ctcf           ;
rename table wgEncodeBroadChipSeqSignalK562H3k27ac         to sav_wgEncodeBroadChipSeqSignalK562H3k27ac        ;
rename table wgEncodeBroadChipSeqSignalK562H3k27me3        to sav_wgEncodeBroadChipSeqSignalK562H3k27me3       ;
rename table wgEncodeBroadChipSeqSignalK562H3k36me3        to sav_wgEncodeBroadChipSeqSignalK562H3k36me3       ;
rename table wgEncodeBroadChipSeqSignalK562H3k4me1         to sav_wgEncodeBroadChipSeqSignalK562H3k4me1        ;
rename table wgEncodeBroadChipSeqSignalK562H3k4me2         to sav_wgEncodeBroadChipSeqSignalK562H3k4me2        ;
rename table wgEncodeBroadChipSeqSignalK562H3k4me3         to sav_wgEncodeBroadChipSeqSignalK562H3k4me3        ;
rename table wgEncodeBroadChipSeqSignalK562H3k9ac          to sav_wgEncodeBroadChipSeqSignalK562H3k9ac         ;
rename table wgEncodeBroadChipSeqSignalK562H3k9me1         to sav_wgEncodeBroadChipSeqSignalK562H3k9me1        ;
rename table wgEncodeBroadChipSeqSignalK562H4k20me1        to sav_wgEncodeBroadChipSeqSignalK562H4k20me1       ;
rename table wgEncodeBroadChipSeqSignalK562Pol2b           to sav_wgEncodeBroadChipSeqSignalK562Pol2b          ;

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/149 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/149 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/149 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/150 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/151 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/152 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/153 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/154 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/155 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/156 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/157 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/158 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/159 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/160 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/161 > validate_error 2>&1

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/150 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/150 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/151 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/151 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/152 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/152 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/153 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/153 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/154 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/154 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/155 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/155 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/156 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/156 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/157 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/157 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/158 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/158 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/159 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/159 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/160 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/160 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/161 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/161 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/173 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/174 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/175 > validate_error 2>&1

tar -cpzf redoHuvecControl.tgz BroadChipSeqControl.DAF BroadChipSeqControl.DDF 
mv redoHuvecControl.tgz ../../ftp/prod/tarjei/ 

tar -cpzf redoNHekH3K4me3.tgz BroadChipSeq.DDF 
mv redoNHekH3K4me3.tgz ../../ftp/prod/tarjei/ 

tar -cpzf redoNHekH3K4me2.tgz BroadChipSeq.DDF 
mv redoNHekH3K4me2.tgz ../../ftp/prod/tarjei/ 

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /cluster/data/encode/pipeline/encpipeline_prod/185 > validate_error 2>&1

tar -cpzf redoKeratinocyteControl.tgz BroadChipSeqControl.DAF BroadChipSeqControl.DDF 
mv redoKeratinocyteControl.tgz ../../ftp/prod/tarjei/ 

Last in trachkDb.ra: 160, 181

Broad first release to RR 4/6/2009
==================================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 140 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 141 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 142 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 143 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 144 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 145 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 146 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 147 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 148 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 149 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 150 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 151 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 152 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 153 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 154 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 155 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 156 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 157 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 158 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 159 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 160 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 161 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 162 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 163 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 164 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 165 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 166 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 167 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 168 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 169 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 170 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 171 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 172 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 173 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 174 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 175 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 176 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 177 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 178 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 179 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 180 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 181 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 182 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 183 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 184 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 185 released

Investigation of bedItemOverlapCount bug 2009-05-01
====================================================

/cluster/bin/x86_64/bedExtendRanges hg18 300 data/Broad_Raw_GM12878_H3K4me1_rep1_chr22.bed data/Broad_Raw_GM12878_H3K4me1_rep1_chrX.bed | sort  -S 5G  -T /data/tmp -k1,1 -k2,2n  > manualSort.bed 
bedItemOverlapCount -verbose=2 hg18 manualSort.bed > manualRawSignal1.bed 
~/bin/x86_64/bedItemOverlapCount -verbose=2 hg18 manualSort.bed > manualRawSignal1.bed 
/cluster/bin/x86_64/bedExtendRanges hg18 300 data/Broad_Raw_GM12878_H3K4me1_rep1_chr22.bed data/Broad_Raw_GM12878_H3K4me1_rep1_chrX.bed | sort  -S 5G  -T /data/tmp -k1,1 -k2,2n  - | grep -v -E "^track" | bedItemOverlapCount -verbose=2 hg18 stdin > manualRawSignal1.bed 


Regenerate Raw Signals because of bug in bedOverlap 2009-05-11
==============================================================
# Can't rename sig because wigs are attached to files.  The regeneration will merely add some data to the end of chrX.  
# Could fly without a net and regen to the same name or could regen to Rel2, even though there is no real difference.
# Regen to Rel to requires release alpha/beta but so be it.  List of table:
subId=140 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me3  fragLength=300
subId=140 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3  fragLength=300
subId=141 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me2  fragLength=300
subId=141 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2  fragLength=300
subId=142 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me1  fragLength=300
subId=142 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1  fragLength=300
subId=143 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k36me3 fragLength=300
subId=143 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3 fragLength=300
subId=144 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27me3 fragLength=300
subId=144 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3 fragLength=300
subId=145 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27ac  fragLength=300
subId=145 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27ac  fragLength=300
subId=146 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k9ac   fragLength=300
subId=146 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9ac   fragLength=300
subId=147 wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1 fragLength=300
subId=147 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1 fragLength=300
subId=148 wgEncodeBroadChipSeqAlignmentsRep1Gm12878Ctcf     fragLength=300
subId=148 wgEncodeBroadChipSeqAlignmentsRep2Gm12878Ctcf     fragLength=300
subId=149 wgEncodeBroadChipSeqAlignmentsRep1Gm12878Control  fragLength=300
subId=149 wgEncodeBroadChipSeqAlignmentsRep2Gm12878Control  fragLength=300
subId=150 wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me3     fragLength=300
subId=150 wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me3     fragLength=300
subId=151 wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me2     fragLength=300
subId=151 wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me2     fragLength=300
subId=152 wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me1     fragLength=300
subId=152 wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me1     fragLength=300
subId=153 wgEncodeBroadChipSeqAlignmentsRep1K562H3k27me3    fragLength=300
subId=153 wgEncodeBroadChipSeqAlignmentsRep2K562H3k27me3    fragLength=300
subId=154 wgEncodeBroadChipSeqAlignmentsRep1K562H3k36me3    fragLength=300
subId=154 wgEncodeBroadChipSeqAlignmentsRep2K562H3k36me3    fragLength=300
subId=155 wgEncodeBroadChipSeqAlignmentsRep1K562H3k9ac      fragLength=300
subId=155 wgEncodeBroadChipSeqAlignmentsRep2K562H3k9ac      fragLength=300
subId=156 wgEncodeBroadChipSeqAlignmentsRep1K562H3k27ac     fragLength=300
subId=156 wgEncodeBroadChipSeqAlignmentsRep2K562H3k27ac     fragLength=300
subId=157 wgEncodeBroadChipSeqAlignmentsRep1K562Ctcf        fragLength=300
subId=157 wgEncodeBroadChipSeqAlignmentsRep2K562Ctcf        fragLength=300
subId=158 wgEncodeBroadChipSeqAlignmentsRep1K562H3k9me1     fragLength=300
subId=158 wgEncodeBroadChipSeqAlignmentsRep2K562H3k9me1     fragLength=300
subId=159 wgEncodeBroadChipSeqAlignmentsRep1K562H4k20me1    fragLength=300
subId=159 wgEncodeBroadChipSeqAlignmentsRep2K562H4k20me1    fragLength=300
subId=160 wgEncodeBroadChipSeqAlignmentsRep1K562Pol2b       fragLength=300
subId=160 wgEncodeBroadChipSeqAlignmentsRep2K562Pol2b       fragLength=300
subId=161 wgEncodeBroadChipSeqAlignmentsRep1K562Control     fragLength=300
subId=161 wgEncodeBroadChipSeqAlignmentsRep2K562Control     fragLength=300
subId=162 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me3    fragLength=300
subId=162 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3    fragLength=300
subId=163 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me2    fragLength=300
subId=163 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me2    fragLength=300
subId=164 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me1    fragLength=300
subId=164 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1    fragLength=300
subId=165 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27me3   fragLength=300
subId=165 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3   fragLength=300
subId=166 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k36me3   fragLength=300
subId=166 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3   fragLength=300
subId=167 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9ac     fragLength=300
subId=167 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9ac     fragLength=300
subId=168 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27ac    fragLength=300
subId=168 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27ac    fragLength=300
subId=169 wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9me1    fragLength=300
subId=169 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9me1    fragLength=300
subId=170 wgEncodeBroadChipSeqAlignmentsRep1HuvecH4k20me1   fragLength=300
subId=170 wgEncodeBroadChipSeqAlignmentsRep2HuvecH4k20me1   fragLength=300
subId=171 wgEncodeBroadChipSeqAlignmentsRep1HuvecCtcf       fragLength=300
subId=171 wgEncodeBroadChipSeqAlignmentsRep2HuvecCtcf       fragLength=300
subId=172 wgEncodeBroadChipSeqAlignmentsRep1HuvecPol2b      fragLength=300
subId=172 wgEncodeBroadChipSeqAlignmentsRep2HuvecPol2b      fragLength=300
subId=173 wgEncodeBroadChipSeqAlignmentsRep1HuvecControl    fragLength=300
subId=173 wgEncodeBroadChipSeqAlignmentsRep2HuvecControl    fragLength=300
subId=174 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me3     fragLength=300
subId=174 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me3     fragLength=300
subId=175 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me2     fragLength=300
subId=175 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me2     fragLength=300
subId=176 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me1     fragLength=300
subId=176 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me1     fragLength=300
subId=177 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k27me3    fragLength=300
subId=177 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k27me3    fragLength=300
subId=178 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k36me3    fragLength=300
subId=178 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k36me3    fragLength=300
subId=179 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k9ac      fragLength=300
subId=179 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k9ac      fragLength=300
subId=180 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k27ac     fragLength=300
subId=180 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k27ac     fragLength=300
subId=181 wgEncodeBroadChipSeqAlignmentsRep1NhekH3k9me1     fragLength=300
subId=181 wgEncodeBroadChipSeqAlignmentsRep2NhekH3k9me1     fragLength=300
subId=182 wgEncodeBroadChipSeqAlignmentsRep1NhekH4k20me1    fragLength=300
subId=182 wgEncodeBroadChipSeqAlignmentsRep2NhekH4k20me1    fragLength=300
subId=183 wgEncodeBroadChipSeqAlignmentsRep1NhekCtcf        fragLength=300
subId=183 wgEncodeBroadChipSeqAlignmentsRep2NhekCtcf        fragLength=300
subId=184 wgEncodeBroadChipSeqAlignmentsRep1NhekPol2b       fragLength=300
subId=184 wgEncodeBroadChipSeqAlignmentsRep2NhekPol2b       fragLength=300
subId=185 wgEncodeBroadChipSeqAlignmentsRep1NhekControl     fragLength=300
subId=185 wgEncodeBroadChipSeqAlignmentsRep2NhekControl     fragLength=300

List of submission dirs: 140-185
# make rawSigBroad.D*F
tar -cpzf rawSigBroad.tgz rawSigBroad.D*F
Made new submission dir=332

# Move superceded dir out of the way:
cd encpipeline_prod
mv 66 superceded/
mv 108 superceded/

validate errors:
ERROR: failed validateTagAlign : Error [file=../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr11.bed, line=229165]: end(134452385) > chromSize(chr11=134452384) [chr11     134452333       134452385       TAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG     1000    +]
Aborting ... found 1 errors in total


grep chromSize validate_error | grep -v chr11 | grep -v chr7 | grep -v chr10 | grep -v chr15 | grep -v chr21 | grep -v chr18 | grep -v chrX| wc -l
0
chr7,chr10,chr15,chr10,chr11,chr18,chr21
Sequences length 51, end - start = 52  Bad news

Are they all 51/52?
awk '{printf "%d\n",$3 - $2;}' ../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr1.bed | uniq -c | wc -l
1
awk '{printf "%d\n",$3 - $2;}' ../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr1.bed | head
52
52
head ../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr1.bed       
chr1    68004439        68004491        AGACAAGCCCCTTTCAACGTCCCACCCAATTATCGGCTGACAAACTTTCCA     1000    +
chr1    216184249       216184301       CTATAATCCCAGCTACTTGGAAGGCTGAGGCAGGAGAATCGCTTGAACCTG     1000    -
head ../140/data/Broad_Raw_GM12878_H3K4me3_rep1_chr1.bed | awk '{printf "%s\t%d\t%d\t%s\t%d\t%s\n",$1,$2,$3 - 1,$4,$5,$6;}' 
chr1    68004439        68004490        AGACAAGCCCCTTTCAACGTCCCACCCAATTATCGGCTGACAAACTTTCCA     1000    +
chr1    216184249       216184300       CTATAATCCCAGCTACTTGGAAGGCTGAGGCAGGAGAATCGCTTGAACCTG     1000    -

### So it appears that all Broad tagAlign files have and end position 1 past where it should be !!!
# it also appears that this can be remedied here, but not without a lot of processing.
 
# created 332/fixTagAlign.sh script for all of the Broad tagAlign files 

Generate RawSignal files for download 2009-5-28
===============================================
from pip
grep RawSignal 332/out/load.ra | grep auto >> 325/out/mkRawSigsFiles.sh 
grep RawSignal 332/out/load.ra | grep wgEncode >> 325/out/mkRawSigsFiles.sh 
...
Edit and then run 332/out/mkRawSigsFiles.sh
placing *.wig.gz into downloads/wgEncodeBroadChipSeq/raw
cd downloads/wgEncodeBroadChipSeq/raw
cp ../preamble.html
cp ../fileDb.ra
edit preamble.html to note the subdirectory only contains Raw Signals
encodeDownloadsPage.pl index.html
mkdir old
mv *.tagAlign.gz old
mv ../wgEncodeBoradChipSeqRel2/*.tagAlign.gz .
grep metatdata /hive/groups/encode/dcc/pipeline/encpipeline_prod/332/out/fileDb.ra | grep tagAlign > /hive/groups/encode/dcc/pipeline/encpipeline_prod/332/out/fileDb.tagAgling.ra
# edit /hive/groups/encode/dcc/pipeline/encpipeline_prod/332/out/fileDb.tagAgling.ra 
grep metatdata /hive/groups/encode/dcc/pipeline/encpipeline_prod/332/out/fileDb.tagAgling.ra >> fileDb.ra
encodeDownloadsPage.pl index.html
/cluster/data/encode/pipeline/bin/encodeStatus.pl 332 displayed


Tarjei sends alignability track as tar.gz 2009-06-02
====================================================
# in /cse/staff/tdreszer/docs/ENCODE/broad/mapability
tar -xzf Broad_Alignable.tar.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/107/DukeExtraTracks.DAF broadAlignability.DAF
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/107/DukeExtraTracks.DDF broadAlignability.DDF
# edit DDF and DAF
tar -cpzf broadAlignability.tgz broadAlignability.DAF broadAlignability.DDF Broad_Alignable_chr*.wig
# log into submission page as tarjei and submit this 
rename table wgEncodeBroadMapabilityAlignability36bpReferencegenome to wgEncodeBroadMapabilityAlign36mer;
update wgEncodeBroadMapabilityAlign36mer set file = "/gbdb/hg18/wib/wgEncodeBroadMapabilityAlign36mer.wib";
cd 344
mv wgEncodeBroadMapabilityAlignability36bpReferencegenome.wib wgEncodeBroadMapabilityAlign36mer.wib
rm /gbdb/hg18/wib/wgEncodeBroadMapabilityAlignability36bpReferencegenome.wib
cd /gbdb/hg18/wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/344/wgEncodeBroadMapabilityAlign36mer.wib wgEncodeBroadMapabilityAlign36mer.wib
# in downloads dir: wgEncodeMapability
mv ../wgEncodeBroadMapability/wgEncodeBroadMapabilityAlignability36bpReferencegenome.wib wgEncodeBroadMapabilityAlign36mer.wib
# edit trackDb.wgEncode.ra
make alpha DBS=hg18
encodeDownloadsPage.pl index.html

/cluster/data/encode/pipeline/bin/encodeStatus.pl 344 displayed


# quicky for broad
validateFiles -type=tagAlign -genome=/cluster/data/hg18/hg18.2bit -mismatches=3 -nMatch -matchFirst=25 -mmCheckOneInN=100 wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocytePol2b.tagAlign.gz
Works!

head -2 Broad_Raw_HMEC_CTCF_rep1_chr1.bed       
chr1    13      48      TAACCCTAACCCTAACCCTAACCCTAACCCTAACNC    1000    +
chr1    62      97      AACCCTAACCCTAACCCTAACCCTAACCCTAACCCT    1000    -
head -2 Broad_Raw_HMEC_CTCF_rep1_chr1.bed | awk '{printf "%s\t%d\t%d\t%s\t%d\t%s\n",$1,$2 - 1,$3,$4,$5,$6;}' 
chr1    12      48      TAACCCTAACCCTAACCCTAACCCTAACCCTAACNC    1000    +
chr1    61      97      AACCCTAACCCTAACCCTAACCCTAACCCTAACCCT    1000    -
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation x ../551 

head -2 Broad_Raw_HMEC_CTCF_rep1_chr1new2.bed | awk '{printf "%s\t%d\t%d\t%s\t%d\t+\n",$1,$2,$3,$4,$5;}' 


2009-09-27 Noam Shoresh is loading up for Sept freeze
=====================================================
# First submissions failed on tagAligns
1) Half open error
2) Negative strand was double reversed:

ERROR: failed validateTagAlign : Error [file=data/Broad_Raw_HMEC_CTCF_rep1_chr1new.bed, line=200]: too many mismatches (found 22
/36, maximum is 3) (chr1 15955 15991 -)
seq=[CTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTT]
gen=[aaggaggaactcactgaaaagtgctggcctgaggag]

These are all negative strand problems.  The tagAlign should have the actual sequence that the sequencer came up with.  The same one as found in the fastq (unaligned).  But it looks like you reversed the sequence in both senses of the word.  That is the sequence
  char1 15955 15991 CTCCTCAGGCCAGCACTTTTCAGTGAGTTCCTCCTT -
should have been
  char1 15955 15991 AAGGAGGAACTCACTGAAAAGTGCTGGCCTGAGGAG -
  
Noam fixed these and is resubmitting.  His first one after this loads fine.

Broad also has the outstanding sparse signal error:
From the looks of the data, every *.wig file has a first line something like:
   fixedStep chrom=chr3 start=1 step=25
But should have a first line something like:
   fixedStep chrom=chr3 start=1 step=25 span=25

This means the first value will be set for positions 1-25 and the second will be set for 26-50.  
What Broad is currently submitting will set a value at 1 then 26,....  It will leave positions 2-25 valueless!  
This is not a problem and the Broad signal graphs are still interpretable.  But I believe Broad's intention is 
to show continuous signal across the whole chromosome, but what they are showing is a discrete signal of 
1 base in length at 25 base intervals.

Response from Noam 9-28-2009:
I forgot about the wig files... But it is, in fact, with gaps, that we usually look at these data, so this is intentional.
In a way it might make a bit more sense to change it... but for consistency's sake, and to save me some hassle right now, let's keep it as is.
-tim: Agreed.

2009-10-02 Melissa got the tracks loaded int trackDb
====================================================
select id,name,status from projects where status = "loaded" and name like "Broad%";
| 554 | BroadChipSeq_HMEC_CTCF_092709      | loaded | 
| 558 | BroadChipSeq_HMEC_WCE_092809       | loaded | 
| 559 | BroadChipSeq_HepG2_WCE_092809.tgz  | loaded | 
| 561 | BroadChipSeq_HepG2_H3K9ac_092809   | loaded | 
| 562 | BroadChipSeq_HMEC_H3K27me3_092809  | loaded | 
| 563 | BroadChipSeq_HepG2_CTCF_092809     | loaded | 
| 564 | BroadChipSeq_H1_H3K27me3_092809    | loaded | 
| 565 | BroadChipSeq_HMEC_H3K4me3_092809   | loaded | 
| 566 | BroadChipSeq_H1_H3K4me3_092809     | loaded | 
| 567 | BroadChipSeq_HepG2_H3K36me3_092809 | loaded | 
| 568 | BroadChipSeq_HMEC_H3K36me3_092809  | loaded | 
| 569 | BroadChipSeq_HMEC_H3K9ac_092809    | loaded | 
| 570 | BroadChipSeq_HMEC_H3K27ac_092809   | loaded | 
| 571 | BroadChipSeq_H1_H3K4me1_092809     | loaded | 
| 572 | BroadChipSeq_HepG2_H3K4me2_092809  | loaded | 
| 573 | BroadChipSeq_HMEC_H3K4me2_092809   | loaded | 
| 574 | BroadChipSeq_HMEC_H3K4me1_092809   | loaded | 
| 575 | BroadChipSeq_NHLF_H3K9ac_092809    | loaded | 
| 576 | BroadChipSeq_HepG2_H3K27ac_092809  | loaded | 
| 577 | BroadChipSeq_NHLF_H3K4me1_092809   | loaded | 
| 578 | BroadChipSeq_NHLF_H3K4me3_092809   | loaded | 
| 579 | BroadChipSeq_NHLF_H4K20me1_092809  | loaded | 
| 580 | BroadChipSeq_HMEC_H4K20me1_092809  | loaded | 
| 581 | BroadChipSeq_HepG2_H3K4me3_092809  | loaded | 
| 582 | BroadChipSeq_NHLF_H3K27ac_092809   | loaded | 
| 583 | BroadChipSeq_NHLF_H3K36me3_092809  | loaded | 
| 584 | BroadChipSeq_NHLF_H3K4me2_092809   | loaded | 
| 585 | BroadChipSeq_H1_CTCF_092809        | loaded | 
| 586 | BroadChipSeq_HepG2_H4K20me1_092809 | loaded | 
| 616 | BroadChipSeq_H1_WCE_092809         | loaded | 
| 617 | BroadChipSeq_NHLF_WCE_092809       | loaded | 
| 618 | BroadChipSeq_NHLF_H3K27me3_092809  | loaded | 
| 619 | BroadChipSeq_H1_H4K20me1_092809    | loaded | 

/cluster/data/encode/pipeline/bin/encodeStatus.pl 554 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 558 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 559 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 561 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 562 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 563 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 564 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 565 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 566 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 567 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 568 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 569 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 570 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 571 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 572 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 573 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 574 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 575 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 576 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 577 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 578 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 579 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 580 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 581 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 582 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 583 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 584 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 585 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 586 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 616 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 617 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 618 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 619 displayed

2009-10-07 Noam realized the peaks were wrong
=============================================
Had him submit them all to 1 new dir.
Expected and got validation failed because old tables were in the way
validated the new data only touches unreleased data
modified daf with "allowReloads"
revalidated... loaded fine
/cluster/data/encode/pipeline/bin/encodeStatus.pl 668 displayed
remodified daf to remove "allowReloads" to avoid future accidents

2009-10-09 Aproval
==================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 558 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 332 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 559 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 554 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 561 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 562 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 563 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 564 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 565 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 566 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 567 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 568 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 569 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 571 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 570 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 572 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 573 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 574 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 575 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 576 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 577 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 578 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 579 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 580 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 581 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 582 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 583 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 584 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 585 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 586 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 616 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 617 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 618 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 619 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 668 approved

2009-10-14 Make release1 downloads dir to prepare for release2
==============================================================
cd {downloadsDir}/wgEncodeBroadChIPseq/
mkdir release1
cp preamble.html release1/
cp fileDb.ra release1/
# In RR browser, go to downloads page and save source into release1/ as index.html
# Use that list as complete set of *.gz files that should be in release1
# Attempt to link them from downloads dir.  If this fails, then mv from old:
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878Control.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878Ctcf.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k36me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me2.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k9ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecControl.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecCtcf.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k36me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me2.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecH4k20me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1HuvecPol2b.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562Control.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562Ctcf.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k27ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k27me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k36me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me2.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k9ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H3k9me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562H4k20me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1K562Pol2b.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekControl.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekCtcf.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k27ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k27me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k36me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me2.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k4me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k9ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH3k9me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekH4k20me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep1NhekPol2b.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878Control.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878Ctcf.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecControl.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecCtcf.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me2.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecH4k20me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2HuvecPol2b.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562Control.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562Ctcf.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k27ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k27me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k36me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me2.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k9ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H3k9me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562H4k20me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2K562Pol2b.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekControl.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekCtcf.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k27ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k27me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k36me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me2.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k4me3.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k9ac.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH3k9me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekH4k20me1.tagAlign.gz .
mv ../old/wgEncodeBroadChipSeqAlignmentsRep2NhekPol2b.tagAlign.gz .
ln ../wgEncodeBroadChipSeqPeaksGm12878Ctcf.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksGm12878H3k27ac.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksGm12878H3k27me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksGm12878H3k36me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksGm12878H3k4me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksGm12878H3k4me2.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksGm12878H3k4me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksGm12878H3k9ac.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksGm12878H4k20me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecCtcf.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecH3k27ac.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecH3k27me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecH3k36me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecH3k4me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecH3k4me2.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecH3k4me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecH3k9ac.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecH3k9me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecH4k20me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksHuvecPol2b.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562Ctcf.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562H3k27ac.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562H3k27me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562H3k36me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562H3k4me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562H3k4me2.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562H3k4me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562H3k9ac.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562H3k9me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562H4k20me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksK562Pol2b.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekCtcf.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekH3k27ac.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekH3k27me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekH3k36me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekH3k4me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekH3k4me2.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekH3k4me3.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekH3k9ac.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekH3k9me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekH4k20me1.broadPeak.gz .
ln ../wgEncodeBroadChipSeqPeaksNhekPol2b.broadPeak.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878Control.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878Ctcf.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k27ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k27me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k36me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k4me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k4me2.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k4me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H3k9ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1Gm12878H4k20me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecControl.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecCtcf.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k27ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k27me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k36me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k4me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k4me2.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k4me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k9ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH3k9me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecH4k20me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1HuvecPol2b.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562Control.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562Ctcf.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k27ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k27me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k36me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k4me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k4me2.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k4me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k9ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562H3k9me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562H4k20me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1K562Pol2b.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekControl.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekCtcf.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k27ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k27me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k36me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k4me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k4me2.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k4me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k9ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekH3k9me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekH4k20me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep1NhekPol2b.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878Control.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878Ctcf.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k27ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k27me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k36me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k4me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k4me2.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k4me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H3k9ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2Gm12878H4k20me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecControl.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecCtcf.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k27ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k27me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k36me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k4me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k4me2.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k4me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k9ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH3k9me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecH4k20me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2HuvecPol2b.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562Control.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562Ctcf.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k27ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k27me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k36me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k4me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k4me2.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k4me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k9ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562H3k9me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562H4k20me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2K562Pol2b.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekControl.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekCtcf.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k27ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k27me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k36me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k4me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k4me2.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k4me3.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k9ac.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekH3k9me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekH4k20me1.fastq.gz .
ln ../wgEncodeBroadChipSeqRawDataRep2NhekPol2b.fastq.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878Control.wig.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878Ctcf.wig.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878H3k27ac.wig.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878H3k27me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878H3k36me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878H3k4me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878H3k4me2.wig.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878H3k4me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878H3k9ac.wig.gz .
ln ../wgEncodeBroadChipSeqSignalGm12878H4k20me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecControl.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecCtcf.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecH3k27ac.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecH3k27me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecH3k36me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecH3k4me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecH3k4me2.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecH3k4me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecH3k9ac.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecH3k9me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecH4k20me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalHuvecPol2b.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562Control.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562Ctcf.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562H3k27ac.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562H3k27me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562H3k36me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562H3k4me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562H3k4me2.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562H3k4me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562H3k9ac.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562H4k20me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalK562Pol2b.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekControl.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekCtcf.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekH3k27ac.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekH3k27me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekH3k36me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekH3k4me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekH3k4me2.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekH3k4me3.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekH3k9ac.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekH3k9me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekH4k20me1.wig.gz .
ln ../wgEncodeBroadChipSeqSignalNhekPol2b.wig.gz .
# Notice the only versioned data is the tagAligns.

# Replace "Rel2" with "V2"  (wished I had done this with Yale)
# No tables involved! 
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878Control.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep1Gm12878ControlV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878Ctcf.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep1Gm12878CtcfV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k27ac.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k27me3.tagAlign.gz      wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k27me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k36me3.tagAlign.gz      wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k36me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k4me1.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k4me2.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me2V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k4me3.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k4me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H3k9ac.tagAlign.gz        wgEncodeBroadChipSeqAlignmentsRep1Gm12878H3k9acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1Gm12878H4k20me1.tagAlign.gz      wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecControl.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep1HuvecControlV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecCtcf.tagAlign.gz            wgEncodeBroadChipSeqAlignmentsRep1HuvecCtcfV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k27ac.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k27me3.tagAlign.gz        wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k27me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k36me3.tagAlign.gz        wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k36me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k4me1.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k4me2.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me2V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k4me3.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k4me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k9ac.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH3k9me1.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep1HuvecH3k9me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecH4k20me1.tagAlign.gz        wgEncodeBroadChipSeqAlignmentsRep1HuvecH4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1HuvecPol2b.tagAlign.gz           wgEncodeBroadChipSeqAlignmentsRep1HuvecPol2bV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562Control.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep1K562ControlV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562Ctcf.tagAlign.gz             wgEncodeBroadChipSeqAlignmentsRep1K562CtcfV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k27ac.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep1K562H3k27acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k27me3.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep1K562H3k27me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k36me3.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep1K562H3k36me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k4me1.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k4me2.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me2V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k4me3.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep1K562H3k4me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k9ac.tagAlign.gz           wgEncodeBroadChipSeqAlignmentsRep1K562H3k9acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H3k9me1.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep1K562H3k9me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562H4k20me1.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep1K562H4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1K562Pol2b.tagAlign.gz            wgEncodeBroadChipSeqAlignmentsRep1K562Pol2bV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteControl.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteControlV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteCtcf.tagAlign.gz     wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteCtcfV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k27ac.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k27acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k27me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k36me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k4me1.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k4me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k4me2.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k4me2V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k4me3.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k4me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k9ac.tagAlign.gz   wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH3k9me1.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocyteH4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep1KeratinocytePol2b.tagAlign.gz    wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878Control.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878Ctcf.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep2Gm12878CtcfV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k27ac.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k27me3.tagAlign.gz      wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k36me3.tagAlign.gz      wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k4me1.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k4me2.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k4me3.tagAlign.gz       wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H3k9ac.tagAlign.gz        wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2Gm12878H4k20me1.tagAlign.gz      wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecControl.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep2HuvecControlV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecCtcf.tagAlign.gz            wgEncodeBroadChipSeqAlignmentsRep2HuvecCtcfV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k27ac.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k27me3.tagAlign.gz        wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k36me3.tagAlign.gz        wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k4me1.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k4me2.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me2V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k4me3.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k9ac.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH3k9me1.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecH4k20me1.tagAlign.gz        wgEncodeBroadChipSeqAlignmentsRep2HuvecH4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2HuvecPol2b.tagAlign.gz           wgEncodeBroadChipSeqAlignmentsRep2HuvecPol2bV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562Control.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep2K562ControlV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562Ctcf.tagAlign.gz             wgEncodeBroadChipSeqAlignmentsRep2K562CtcfV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k27ac.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep2K562H3k27acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k27me3.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep2K562H3k27me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k36me3.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep2K562H3k36me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k4me1.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k4me2.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me2V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k4me3.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep2K562H3k4me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k9ac.tagAlign.gz           wgEncodeBroadChipSeqAlignmentsRep2K562H3k9acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H3k9me1.tagAlign.gz          wgEncodeBroadChipSeqAlignmentsRep2K562H3k9me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562H4k20me1.tagAlign.gz         wgEncodeBroadChipSeqAlignmentsRep2K562H4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2K562Pol2b.tagAlign.gz            wgEncodeBroadChipSeqAlignmentsRep2K562Pol2bV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteControl.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteControlV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteCtcf.tagAlign.gz     wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteCtcfV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k27ac.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k27acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k27me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k27me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k36me3.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k36me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k4me1.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k4me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k4me2.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k4me2V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k4me3.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k4me3V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k9ac.tagAlign.gz   wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k9acV2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH3k9me1.tagAlign.gz  wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH3k9me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocyteH4k20me1.tagAlign.gz wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqRel2AlignmentsRep2KeratinocytePol2b.tagAlign.gz    wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAlign.gz
ls *V2.* | wc -l 92
ls *Rel2*.gz | wc -l 0
grep Rel2 fileDb.ra | wc -l  92
grep Rel2 fileDb.ra > tmpRel2.txt
grep -v Rel2 fileDb.ra > fileDb.ra.new
cp fileDb.ra fileDb.ra.2009-10-14
# edit tmpRel2.txt to replace Rel2 with V2 and add 'submittedDataVersion="V2 - corrected off-by-one error in end position"'
cat tmpRel2.txt >> fileDb.ra.new
mv fileDb.ra.new fileDb.ra 
# Add a note to the preamble.html to describe the correction on the older tagAligns, and declare this as a "release 2".
encodeDownloadsPage.pl index.html

#Filter ranges:
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878Ctcf    ; 
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k27ac ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k27me3;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k36me3;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k4me1 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k4me2 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k4me3 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H3k9ac  ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksGm12878H4k20me1;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescCtcf     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescH3k27me3 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescH3k4me1  ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescH3k4me3  ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksH1hescH4k20me1 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2Ctcf      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k27ac   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k36me3  ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k4me2   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k4me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H3k9ac    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHepg2H4k20me1  ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecCtcf       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k27ac    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k27me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k36me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k4me1    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k4me2    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k4me3    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH3k9ac     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHmecH4k20me1   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecCtcf      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k27ac   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k27me3  ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k36me3  ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k4me1   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k4me2   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k4me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k9ac    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH3k9me1   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecH4k20me1  ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksHuvecPol2b     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562Ctcf       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k27ac    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k27me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k36me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k4me1    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k4me2    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k4me3    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k9ac     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H3k9me1    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562H4k20me1   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksK562Pol2b      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekCtcf       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k27ac    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k27me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k36me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k4me1    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k4me2    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k4me3    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k9ac     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH3k9me1    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekH4k20me1   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhekPol2b      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k27ac    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k27me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k36me3   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k4me1    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k4me2    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k4me3    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH3k9ac     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeBroadChipSeqPeaksNhlfH4k20me1   ;
# Result score 1000:1000, signalValue 0:45000 (but too variable to be useful) pValue 0:100, qValue -1:-1

2009-11-05 In QA (some time ago actually)
=========================================
select id,name,status from projects where status not in ("displayed","released","revoked","superseded","reviewing"); | 81 |
/cluster/data/encode/pipeline/bin/encodeStatus.pl 558 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 332 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 559 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 554 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 561 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 562 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 563 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 564 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 565 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 566 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 567 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 568 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 569 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 571 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 570 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 572 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 573 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 574 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 575 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 576 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 577 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 578 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 579 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 580 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 581 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 582 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 583 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 584 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 585 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 586 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 616 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 617 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 618 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 619 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 668 reviewing
select id,name,status from projects where status not in ("displayed","released","revoked","superseded","reviewing"); | 46 |

2009-11-30 Missing GM12878 Rep2 tagAligns!
==========================================
Downloads dir has only one (V2) subId=332
sub 332 regenerated Raw from already submitted tagAligns, so there should be no V2
sub 332 was the old fashion Rel2
downloadsDir/release1 has all original which should be the ones!
ln
ln release1/wgEncodeBroadChipSeqAlignmentsRep2Gm12878*.tagAlign.gz .
### NO THIS is not so:
zcat wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1V2.tagAlign.gz | wl          13632898
zcat release1/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1.tagAlign.gz | wl   13632898
zcat wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1V2.tagAlign.gz | head
chr1    31659966        31660013        GAATGAGATCAGCATAGACAGCACAGAGAGGCAAGAGAGCCTCTCGC 1000    +
zcat release1/wgEncodeBroadChipSeqAlignmentsRep1Gm12878H4k20me1.tagAlign.gz | head
chr1    31659966        31660014        GAATGAGATCAGCATAGACAGCACAGAGAGGCAAGAGAGCCTCTCGC 1000    +
### There is an off by one error.  Therefore all V2s are valid.  
I must remove the ones I just linkined in from release1 and then reload the missing ones!

ls *Rep2Gm12878*.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878Control.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878Ctcf.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878CtcfV2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27ac.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9ac.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1.tagAlign.gz

rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878Control.tagAlign.gz
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878Ctcf.tagAlign.gz
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27ac.tagAlign.gz
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3.tagAlign.gz
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3.tagAlign.gz
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1.tagAlign.gz
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2.tagAlign.gz
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3.tagAlign.gz
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9ac.tagAlign.gz
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1.tagAlign.gz

What is missing exactly?
wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878CtcfV2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.gz
wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign.gz

cd {pip}/332
edit DAF/DDF
tar -cpzf BroadResubmitTagAlignRep2s.tgz rawSigBroad.DAF rawSigBroad.DDF
# submitted to 800
ll *Rep2Gm12878*.tagAlign.gz
-rw-rw-r-- 1 qateam protein 198204132 Nov 30 15:31 wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 235330617 Nov 30 15:02 wgEncodeBroadChipSeqAlignmentsRep2Gm12878CtcfV2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 207339598 Nov 30 15:15 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 225546215 Nov 30 15:13 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 295145342 Nov 30 15:22 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 290389709 Nov 30 15:34 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 197423654 Nov 30 15:08 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 203798428 Nov 30 15:10 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 219338761 Nov 30 15:37 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 268390362 Nov 30 15:39 wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz
ll *Rep2Huvec*.tagAlign.gz
-rw-rw-r-- 2 qateam protein 215910513 May 15  2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecControlV2.tagAlign.gz
-rw-rw-r-- 2 qateam protein 255146612 May 15  2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecCtcfV2.tagAlign.gz
-rw-rw-r-- 2 qateam protein 322322114 May 15  2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27acV2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 387746099 Nov 30 15:19 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 377600984 Nov 30 15:29 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 381183723 Nov 30 15:06 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.gz
-rw-rw-r-- 2 qateam protein 313456944 May 15  2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me2V2.tagAlign.gz
-rw-rw-r-- 1 qateam protein 363716703 Nov 30 15:25 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign.gz
-rw-rw-r-- 2 qateam protein 248141307 May 15  2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz
-rw-rw-r-- 2 qateam protein 281337854 May 15  2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9me1V2.tagAlign.gz
-rw-rw-r-- 2 qateam protein 298025445 May 15  2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecH4k20me1V2.tagAlign.gz
-rw-rw-r-- 2 qateam protein 356263922 May 15  2009 wgEncodeBroadChipSeqAlignmentsRep2HuvecPol2bV2.tagAlign.gz

zcat wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz | head
chr1    84721172        84721223        TGGTTGTCAATGGTCTTGGGTACAGGCTTTGGTGGAGCCTAAGTAAAAGAG     1000    -
zcat release1/wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1.tagAlign.gz | head
chr1    84721172        84721224        TGGTTGTCAATGGTCTTGGGTACAGGCTTTGGTGGAGCCTAAGTAAAAGAG     1000    -
# Off by one has been corrected!
encodeDownloadsPage.pl index.html 
cp index.html release2/
cd release2/

ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.gz  .
ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.gz  .
ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign.gz .
ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.gz .
ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlign.gz  .
ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign.gz  .
ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAlign.gz  .
ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.gz   .
ln ../wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign.gz .
ln ../wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.gz   .
ln ../wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign.gz   .
ln ../wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.gz    .
ln ../wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign.gz    .
# update broadChipSeq.notes.txt in docs
# update pushq entry
# inform Anshul

/cluster/data/encode/pipeline/bin/encodeStatus.pl 800 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 800 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 800 reviewing
# give this submission id back to Broad:
update projects set user_id = 34 where id = 800;

2009-12-25 Kayla noticed munged names in downloadsDir
=====================================================
cd {downloadsDir}/broad
wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAl
wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagA
wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAli
wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlig
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAl
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.
wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign
wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.g
wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign
wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.g
wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign
wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.ta
wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAl

ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAl*
ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagA*
ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAli*
ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.*
ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.*
ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign*
ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.*
ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlig*
ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign*
ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAl*
ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.*
ll wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign*
ll wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.g*
ll wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign*
ll wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.g*
ll wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign*
ll wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.ta*
ll wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAl*

# all full names found (and same sizes as mangled version) found except:
ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAl*
ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagA*
ll wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAli*
ll wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.ta*
ll wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAl*

# remove duplicates
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878ControlV2.tagAlign.
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27acV2.tagAlign.
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k27me3V2.tagAlign
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k36me3V2.tagAlign.
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me1V2.tagAlig
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me2V2.tagAlign
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k4me3V2.tagAl
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H3k9acV2.tagAlign.
rm wgEncodeBroadChipSeqAlignmentsRep2Gm12878H4k20me1V2.tagAlign
rm wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k27me3V2.tagAlign.g
rm wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k36me3V2.tagAlign
rm wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me1V2.tagAlign.g
rm wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k4me3V2.tagAlign

# rename mangled
mv wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAl wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagA wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAli  wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAlign.gz
mv wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.ta   wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.tagAlign.gz
mv wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAl   wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAlign.gz

# link
cd release2/
ln ../wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH3k9me1V2.tagAlign.gz   .
ln ../wgEncodeBroadChipSeqAlignmentsRep1KeratinocyteH4k20me1V2.tagAlign.gz  .
ln ../wgEncodeBroadChipSeqAlignmentsRep1KeratinocytePol2bV2.tagAlign.gz     .
ln ../wgEncodeBroadChipSeqAlignmentsRep2KeratinocyteH4k20me1V2.tagAlign.gz  .
ln ../wgEncodeBroadChipSeqAlignmentsRep2KeratinocytePol2bV2.tagAlign.gz     .
cd ..
# edit fileDb.ra replace "cell=Keratinocyte" with "cell=NHEK"
encodeDownloadsPage.pl index.html
cp index.html release2/ 
cp fileDb.ra release2/ 

2009-12-18 Start of Jan 2010 freeze
===================================
select id,name,status from projects where name like "Broad%" and status = "loaded" order by id;
+-----+----------------------------+--------+
| id  | name                       | status |
+-----+----------------------------+--------+
| 815 | BroadChipSeq_H1_H3K9ac     | loaded | 
| 816 | BroadChipSeq_H1_H3K36me3   | loaded | 
| 817 | BroadChipSeq_H1_H3K4me2    | loaded | 
| 818 | BroadChipSeq_NHLF_CTCF     | loaded | 
| 819 | BroadChipSeq_HSMM_H3K36me3 | loaded | 
| 820 | BroadChipSeq_HSMM_H4K20me1 | loaded | 
| 821 | BroadChipSeq_HSMM_H3K4me1  | loaded | 
| 822 | BroadChipSeq_HSMM_H3K27ac  | loaded | 
| 823 | BroadChipSeq_HSMM_H3K27me3 | loaded | 
| 824 | BroadChipSeq_HSMM_H3K9ac   | loaded | 
| 825 | BroadChipSeq_HSMM_H3K4me2  | loaded | 
| 826 | BroadChipSeq_HSMM_CTCF     | loaded | 
| 827 | BroadChipSeq_HSMM_WCE      | loaded | 
| 828 | BroadChipSeq_HSMM_H3K4me3  | loaded | 
+-----+----------------------------+--------+
14 rows in set (0.00 sec)
# added to trackDb.wgEncode.ra, made alpha

cd {downloadsDir}
cp fileDb.ra fileDb.ra.2009-12-18
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/815/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/816/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/817/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/818/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/819/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/820/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/821/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/822/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/823/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/824/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/825/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/826/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/827/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/828/out/fileDb.ra | grep parentTable >> tmp.txt
# e tmp.txt
cat tmp.txt >> fileDb.ra
# Eliminated 28 duplicate fileNames in fileDb.ra 
encodeDownloadsPage.pl index.html

/cluster/data/encode/pipeline/bin/encodeStatus.pl 815 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 816 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 817 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 818 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 819 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 820 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 821 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 822 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 823 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 824 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 825 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 826 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 827 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 828 displayed

# missing tables on RR
 HMEC    H3K4me3         Signal  wgEncodeBroadChipSeqSignalHmecH3k4me3
 HMEC    H3K9ac          Signal  wgEncodeBroadChipSeqSignalHmecH3k9ac
 HMEC    H4K20me1        Signal  wgEncodeBroadChipSeqSignalHmecH4k20me1
 NHLF    H3K27ac         Signal  wgEncodeBroadChipSeqSignalNhlfH3k4me1
 NHLF    H3K27me3        Signal  wgEncodeBroadChipSeqSignalNhlfH3k4me2
 NHLF    H3K36me3        Signal  wgEncodeBroadChipSeqSignalNhlfH3k4me3
 NHLF    H3K4me1         Signal  wgEncodeBroadChipSeqSignalNhlfH3k9ac
 NHLF    H3K4me2         Signal  wgEncodeBroadChipSeqSignalNhlfH3k27ac
 NHLF    H3K4me3         Signal  wgEncodeBroadChipSeqSignalNhlfH3k27me3
 NHLF    H3K9ac          Signal  wgEncodeBroadChipSeqSignalNhlfH3k36me3
 NHLF    H4K20me1        Signal  wgEncodeBroadChipSeqSignalNhlfH4k20me1
 NHLF    Input Control   Signal  wgEncodeBroadChipSeqSignalNhlfControl

/cluster/data/encode/pipeline/bin/encodeStatus.pl 332 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 344 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 554 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 558 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 559 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 561 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 562 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 563 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 564 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 565 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 566 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 567 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 568 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 569 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 570 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 571 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 572 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 573 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 574 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 575 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 576 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 577 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 578 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 579 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 580 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 581 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 582 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 583 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 584 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 585 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 586 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 616 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 617 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 618 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 619 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 668 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 800 released

2010-01-06 Redo the H1s by request from Noam
============================================
# In pipeline website unload 815,816,817 (which were marked as displayed)
Noam resubmitted. validation failed because of trackDb entries
# DANGEROUS: in hgsql hg18
select count(*) from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k36me3'; 2
delete from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k36me3';
select count(*) from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k4me2'; 2
delete from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k4me2';
select count(*) from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k9ac'; 2
delete from trackDb where tableName like 'wgEncodeBroadChipSeq%H1hescH3k9ac';
# restart in pipeline: successful this time. 
make alpha DBS=hg18
/cluster/data/encode/pipeline/bin/encodeStatus.pl 815 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 816 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 817 displayed

## At the freeze:
select id,name,status,user_id,created_at from projects where status = "displayed" and name like "Broad%" and created_at > date('2009-11-01') order by name;
+-----+----------------------------+-----------+---------+---------------------+
| id  | name                       | status    | user_id | created_at          |
+-----+----------------------------+-----------+---------+---------------------+
| 816 | BroadChipSeq_H1_H3K36me3   | displayed |      34 | 2009-12-16 08:20:35 | 
| 817 | BroadChipSeq_H1_H3K4me2    | displayed |      34 | 2009-12-16 08:37:58 | 
| 815 | BroadChipSeq_H1_H3K9ac     | displayed |      34 | 2009-12-16 06:28:45 | 
| 826 | BroadChipSeq_HSMM_CTCF     | displayed |      34 | 2009-12-16 08:44:21 | 
| 822 | BroadChipSeq_HSMM_H3K27ac  | displayed |      34 | 2009-12-16 08:41:44 | 
| 823 | BroadChipSeq_HSMM_H3K27me3 | displayed |      34 | 2009-12-16 08:42:36 | 
| 819 | BroadChipSeq_HSMM_H3K36me3 | displayed |      34 | 2009-12-16 08:39:18 | 
| 821 | BroadChipSeq_HSMM_H3K4me1  | displayed |      34 | 2009-12-16 08:40:59 | 
| 825 | BroadChipSeq_HSMM_H3K4me2  | displayed |      34 | 2009-12-16 08:43:37 | 
| 828 | BroadChipSeq_HSMM_H3K4me3  | displayed |      34 | 2009-12-16 08:45:20 | 
| 824 | BroadChipSeq_HSMM_H3K9ac   | displayed |      34 | 2009-12-16 08:43:09 | 
| 820 | BroadChipSeq_HSMM_H4K20me1 | displayed |      34 | 2009-12-16 08:40:07 | 
| 827 | BroadChipSeq_HSMM_WCE      | displayed |      34 | 2009-12-16 08:44:54 | 
| 818 | BroadChipSeq_NHLF_CTCF     | displayed |      34 | 2009-12-16 08:38:40 | 
+-----+----------------------------+-----------+---------+---------------------+
14 rows

### Post call issues?
None!

/cluster/data/encode/pipeline/bin/encodeStatus.pl 815 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 816 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 817 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 818 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 819 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 820 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 821 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 822 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 823 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 824 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 825 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 826 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 827 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 828 approved

2010-03-01 Prepare for release 3
================================
cd downloadsDir
mkdir release3
# todo:
cd release3
ln ../*.gz .
cp ../index.html .
cp ../protocol.html .
cp ../files.txt .
cp ../md5sum.txt .
cp ../fileDb.ra .
ll *.gz > ../tmp3.txt
cd ../release2
ll *.gz > ../tmp2.txt
cd ..
diff -w tmp2.txt tmp3.txt | grep "<" > tmpOld.txt
diff -w tmp2.txt tmp3.txt | grep ">" > tmpNew.txt
e tmpOld.txt tmpNew.txt # remove the < & >
diff -w tmp3.txt tmpNew.txt | grep "<" > tmpSame.txt

e tmpOld.txt tmpNew.txt 

/cluster/data/encode/pipeline/bin/encodeStatus.pl 818  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 817  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 816  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 815  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 819  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 820  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 821  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 822  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 823  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 824  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 825  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 826  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 827  reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 828  reviewing

/cluster/data/encode/pipeline/bin/encodeStatus.pl 818 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 817 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 816 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 815 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 819 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 820 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 821 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 822 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 823 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 824 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 825 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 826 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 827 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 828 released

2010-04-13 Loadeing metaTbl for hg18
====================================
cd {tdb}
grep metadata trackdDb.wgencode.ra | grep Broad > testing/metaBroad.txt
cd testing
# edit remove the dups
mdbUpdate hg18 metaBroad.txt

cd {downloads}
mdbUpdate hg18 fileDb.ra
Using table named 'hg18.mdb_tdreszer'.
The same variable appears twice: submittedDataVersion="V2 - corrected off-by-one error in end position" and submittedDataVersion="V2 - corrected off-by-one error in end position".  Ignoring second value.
        project=wgEncode grant=Bernstein lab=Broad dataType=ChipSeq cell=HUVEC antibody=H3K9ac fragLength=300 view=Alignments replicate=2 dataVersion="ENCODE Feb 2009 Freeze" subId=332 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 dateResubmitted=2009-05-15 composite=wgEncodeBroadChipSeq parentTable=wgEncodeBroadChipSeqRawSignalRep2HuvecH3k9acV2 fileName=wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz
The same variable appears twice: dateSubmitted=2009-01-06 and dateSubmitted=2009-01-06.  Ignoring second value.
        project=wgEncode grant=Bernstein lab=Broad dataType=ChipSeq cell=HUVEC antibody=H3K9ac fragLength=300 view=Alignments replicate=2 dataVersion="ENCODE Feb 2009 Freeze" subId=332 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 dateResubmitted=2009-05-15 composite=wgEncodeBroadChipSeq parentTable=wgEncodeBroadChipSeqRawSignalRep2HuvecH3k9acV2 fileName=wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz
The same variable appears twice: dateUnrestricted=2009-10-06 and dateUnrestricted=2009-10-06.  Ignoring second value.
        project=wgEncode grant=Bernstein lab=Broad dataType=ChipSeq cell=HUVEC antibody=H3K9ac fragLength=300 view=Alignments replicate=2 dataVersion="ENCODE Feb 2009 Freeze" subId=332 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 submittedDataVersion="V2 - corrected off-by-one error in end position" dateSubmitted=2009-01-06 dateUnrestricted=2009-10-06 dateResubmitted=2009-05-15 composite=wgEncodeBroadChipSeq parentTable=wgEncodeBroadChipSeqRawSignalRep2HuvecH3k9acV2 fileName=wgEncodeBroadChipSeqAlignmentsRep2HuvecH3k9acV2.tagAlign.gz
Read 526 metadata objects from hg18
Affected 7792 row(s) in hg18.mdb_tdreszer

encodeDownloadsPage.pl -mdb=mdb_tdreszer mdb.html .
encodeDownloadsPage.pl -noMdb noMdb.html .
wl mdb.html noMdb.html 
   586 mdb.html
   586 noMdb.html
diff mdb.html noMdb.html 
# Only difference is error in old metadata

cd {tdb}/testing
mdbPrint hg18 -vars="lab=Broad" -ra > mdbBroad.ra
Using table named 'hg18.mdb_tdreszer'.
objects:641  vars:10531

# Expected 549  Difference?  Must be versioned tables and files which were in fileDb.ra but are no longer in the downloads dir. 
# Clean extra entries?

# get downloads dir list
cd {downloads}
ls -1 *.gz | sort > ~/kent/src/hg/makeDb/trackDb/human/hg18/testing/tmp.txt

# get metaTbl list
cd {tdb}/testing
grep metaObject mdbBroad.ra > tmp2.txt
# edit tmp.txt tmp2.txt to strip down to obj names
diff tmp.txt tmp2.txt > tmp3.txt
# edit tmp3.txt to strip down to obj names
wl tmp3.txt
92 tmp3.txt

#edit tmp3.txt as: metadata wgEncodeBroadChipSeqAlignmentsRep1Gm12878Control delete
mdbUpdate hg18 tmp3.txt
Affected 3999 row(s) in hg18.metaTbl_tdreszer

mdbPrint hg18 -vars="lab=Broad" -ra > mdbBroad.ra
Using table named 'hg18.mdb_tdreszer'.
objects:549  vars:8967

cd {downloads}
encodeDownloadsPage.pl -mdb=mdb_tdreszer mdbNew.html .
diff mdb.html mdbNew.html
# no difference

cd {tdb}/testing
mv testing/mdbBroad.ra .
mdbUpdate hg18 -table=mdb mdbBroad.ra 
Read 549 metadata objects from hg18
Affected 6228 row(s) in hg18.mdb

cvs ci mdbBroad.ra


2010-04-23 Standardize to setType, inputType
============================================
mdbPrint hg18 -vars="lab=Broad" -countObjs                 
Using table named 'hg18.mdb_tdreszer'.
549 objects
mdbUpdate hg18 -vars="lab=Broad antibody=Input" -var=setType -val=input      
Using table named 'hg18.mdb_tdreszer'.
Affected 45 row(s) in hg18.mdb_tdreszer
mdbUpdate hg18 -vars="lab=Broad antibody!=Input" -var=setType -val=exp      
Using table named 'hg18.mdb_tdreszer'.
Affected 504 row(s) in hg18.mdb_tdreszer

#mdbUpdate hg18 -vars="lab=Broad setType=input" -var=inputType -val=?? -test
#mdbUpdate hg18 -vars="lab=Broad setType=exp" -var=setType -val=exp -test

select distinct t1.val cell,t2.val antibody from mdb_tdreszer t1,mdb_tdreszer t2 where t1.obj like "wgEncodeBroad%"
 and t1.obj = t2.obj
 and t1.var = "cell" and t2.var = "antibody"
 order by t1.val,t2.val;
93 rows in set (0.05 sec)

select distinct t1.val cell from mdb_tdreszer t1 where t1.obj like "wgEncodeBroad%"
 and t1.var = "cell"
 order by t1.val;
+---------+
| cell    |
+---------+
| GM12878 | 
| H1-hESC | 
| HMEC    | 
| HSMM    | 
| HUVEC   | 
| HepG2   | 
| K562    | 
| NHEK    | 
| NHLF    | 
+---------+
9 rows in set (0.03 sec)
mdbUpdate hg18 -vars="lab=Broad cell=GM12878" -var=inputType val=GM12878/Input
mdbUpdate hg18 -vars="lab=Broad cell=H1-hESC" -var=inputType val=H1-hESC/Input
mdbUpdate hg18 -vars="lab=Broad cell=HMEC   " -var=inputType val=HMEC/Input
mdbUpdate hg18 -vars="lab=Broad cell=HSMM   " -var=inputType val=HSMM/Input
mdbUpdate hg18 -vars="lab=Broad cell=HUVEC  " -var=inputType val=HUVEC/Input
mdbUpdate hg18 -vars="lab=Broad cell=HepG2  " -var=inputType val=HepG2/Input
mdbUpdate hg18 -vars="lab=Broad cell=K562   " -var=inputType val=K562/Input
mdbUpdate hg18 -vars="lab=Broad cell=NHEK   " -var=inputType val=NHEK/Input
mdbUpdate hg18 -vars="lab=Broad cell=NHLF   " -var=inputType val=NHLF/Input
Affected 59 row(s) in hg18.mdb_tdreszer
Affected 53 row(s) in hg18.mdb_tdreszer
Affected 59 row(s) in hg18.mdb_tdreszer
Affected 59 row(s) in hg18.mdb_tdreszer
Affected 71 row(s) in hg18.mdb_tdreszer
Affected 47 row(s) in hg18.mdb_tdreszer
Affected 71 row(s) in hg18.mdb_tdreszer
Affected 71 row(s) in hg18.mdb_tdreszer
Affected 59 row(s) in hg18.mdb_tdreszer
Total: 549
mdbPrint hg18 -vars="lab=Broad" > mdbBroad.ra
Using table named 'hg18.mdb_tdreszer'.
objects:549  vars:10065
mdbUpdate hg18 table=mdb mdbBroad.ra
Read 549 metadata objects from hg18
Affected 1098 row(s) in hg18.mdb
cvs ci -m "Extended setType and inputType to Broad" mdbBroad.ra
cd {downloadsDir}
encodeDownloadsPage.pl -mdb=mdb index.html .


2011-01-21 Broad Chromatin Modelling by HMM for hg18 
====================================================
Submitted to 3446
Changed Encode.pm to accept hg18
Changed some DDF and failed on dataType=ChipSeq requiring an antibody.  Changed to dataTypeCombined
doEncodeValidate worked so sent it through the pipeline.  Loaded!
# verified tables exist in hg18 and downloadable files are in hg18  Tables are "bed 9"
show tables like "wgEncodeBroadHmm%";
+------------------------------------+
| wgEncodeBroadHmmGm12878HMM         | 
| wgEncodeBroadHmmH1hescHMM          | 
| wgEncodeBroadHmmHepg2HMM           | 
| wgEncodeBroadHmmHmecHMM            | 
| wgEncodeBroadHmmHsmmHMM            | 
| wgEncodeBroadHmmHuvecHMM           | 
| wgEncodeBroadHmmK562HMM            | 
| wgEncodeBroadHmmNhekHMM            | 
| wgEncodeBroadHmmNhlfHMM            | 
+------------------------------------+
select min(score),max(score) from wgEncodeBroadHmmH1hescHMM;
+------------+------------+
| min(score) | max(score) |
+------------+------------+
|          0 |          0 | 
+------------+------------+
cd {downloadsHg18}/wgEncodeBroadHmm
ll wgEncode*
-rw-rw-r--   1 encodeteam protein 5305015 Jan 21 09:39 wgEncodeBroadHmmGm12878HMM.bed.gz
-rw-rw-r--   1 encodeteam protein 5717187 Jan 21 09:39 wgEncodeBroadHmmH1hescHMM.bed.gz
-rw-rw-r--   1 encodeteam protein 5097678 Jan 21 09:39 wgEncodeBroadHmmHepg2HMM.bed.gz
-rw-rw-r--   1 encodeteam protein 5653968 Jan 21 09:39 wgEncodeBroadHmmHmecHMM.bed.gz
-rw-rw-r--   1 encodeteam protein 5956576 Jan 21 09:39 wgEncodeBroadHmmHsmmHMM.bed.gz
-rw-rw-r--   1 encodeteam protein 5144281 Jan 21 09:39 wgEncodeBroadHmmHuvecHMM.bed.gz
-rw-rw-r--   1 encodeteam protein 5785441 Jan 21 09:38 wgEncodeBroadHmmK562HMM.bed.gz
-rw-rw-r--   1 encodeteam protein 5854057 Jan 21 09:38 wgEncodeBroadHmmNhekHMM.bed.gz
-rw-rw-r--   1 encodeteam protein 5970587 Jan 21 09:38 wgEncodeBroadHmmNhlfHMM.bed.gz

edit trackDb.ra template and place it in trackDb/human/hg18/wgEncodeBroadHmm
cd trackDb/
make DBS=hg18
# see them there

# now metadata
cd {pip}/3446
mdbUpdate hg18 out/mdb.txt

# Check in changes:
cd .. {hg18/metaDb/alpha}
mdbPrint hg18 -vars="composite=wgEncodeBroadHmm" > wgEncodeBroadHmm.ra
Using table named 'hg18.metaDb_tdreszer'.
objects:9  vars:135
gadd wgEncodeBroadHmm.ra
cd ../../ (hg18)
gadd wgEncodeBroadHmm.ra
gadd trackDb.wgEncode.ra

git: ci, up, push
cd ../../ (trackDb)
make DBS=hg18; make alpha DBS=hg18


git: up, add, ci, up, push
cd ../../../../ (trackDb)
make DBS=hg18; make alpha DBS=hg18

cd {downloadsHg18}/wgEncodeBroadHmm
encodeDownloadsPage.pl -db=hg18 index.html
# 9 files.  No metadata  # 9 found in hgFileUi

#neglected to add mdb ra to make file
cd .. {hg18/metaDb/alpha}
e makefile
git: up, add, ci, up, push
cd ../../../../ (trackDb)
make DBS=hg18; make alpha DBS=hg18

cd {downloadsHg18}/wgEncodeBroadHmm
encodeDownloadsPage.pl -db=hg18 index.html
# 9 files.  Full metadata  # 9 found in hgFileUi

/cluster/data/encode/pipeline/bin/encodeStatus.pl 3446 displayed

2011-01-24 Corrections to names
===============================
12345678901234567
1 Active Promoter
2 Weak Promoter
3 Poised Promoter
4 Strong Enhancer
5 Strong Enhancer
6 Weak Enhancer
7 Weak Enhancer
8 Insulator
9 Txn Transition
10 Txn Elongation
11 Weak Txn
12 Repressed
13 Heterochrom/lo
14 Repetitive/CNV
15 Repetitive/CNV

1) Ideally lab resubmits proper beds
2) hardest: possibly edit bed files, then reload
3) Easiest: update tables
show tables like "wgEncodeBroadHmm%";
| wgEncodeBroadHmmGm12878HMM         | 
| wgEncodeBroadHmmH1hescHMM          | 
| wgEncodeBroadHmmHepg2HMM           | 
| wgEncodeBroadHmmHmecHMM            | 
| wgEncodeBroadHmmHsmmHMM            | 
| wgEncodeBroadHmmHuvecHMM           | 
| wgEncodeBroadHmmK562HMM            | 
| wgEncodeBroadHmmNhekHMM            | 
| wgEncodeBroadHmmNhlfHMM            | 
select distinct name from wgEncodeBroadHmmGm12878HMM order by name;
select distinct name from wgEncodeBroadHmmH1hescHMM order by name;
select distinct name from wgEncodeBroadHmmHepg2HMM order by name;
select distinct name from wgEncodeBroadHmmHmecHMM order by name;
select distinct name from wgEncodeBroadHmmHsmmHMM order by name;
select distinct name from wgEncodeBroadHmmHuvecHMM order by name;
select distinct name from wgEncodeBroadHmmK562HMM order by name;
select distinct name from wgEncodeBroadHmmNhekHMM order by name;
select distinct name from wgEncodeBroadHmmNhlfHMM order by name;
# All are 1-15 as expected
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | wl
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | wl
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | wl
zcat wgEncodeBroadHmmHmecHMM.bed.gz | wl
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | wl
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | wl
zcat wgEncodeBroadHmmK562HMM.bed.gz | wl
zcat wgEncodeBroadHmmNhekHMM.bed.gz | wl
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | wl

zcat wgEncodeBroadHmmGm12878HMM.bed.gz | wl 570580
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | wl 618287
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | wl 545647
zcat wgEncodeBroadHmmHmecHMM.bed.gz | wl 608568
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | wl 638307
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | wl 549178
zcat wgEncodeBroadHmmK562HMM.bed.gz | wl 621678
zcat wgEncodeBroadHmmNhekHMM.bed.gz | wl 627623
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | wl 640298

# Could zcat wgEncodeBroadHmmNhlfHMM.bed.gz | h | grep -P "\t10\t0\t\." > wgEncodeBroadHmmNhlfHMM.bed.1 
# Could
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | h | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./' 

rm   wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./'    >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./'      >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./'    >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./'          >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./'     >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./'  >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./'        >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./'       >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed
zcat wgEncodeBroadHmmGm12878HMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmGm12878HMM.bed

rm   wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./'    >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./'      >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./'    >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./'          >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./'     >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./'  >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./'        >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./'       >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed
zcat wgEncodeBroadHmmH1hescHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmH1hescHMM.bed

rm   wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./'    >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./'      >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./'    >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./'          >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./'     >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./'  >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./'        >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./'       >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed
zcat wgEncodeBroadHmmHepg2HMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHepg2HMM.bed

rm   wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./'    >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./'      >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./'    >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./'          >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./'     >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./'  >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./'        >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./'       >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed
zcat wgEncodeBroadHmmHmecHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHmecHMM.bed

rm   wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./'    >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./'      >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./'    >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./'          >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./'     >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./'  >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./'        >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./'       >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed
zcat wgEncodeBroadHmmHsmmHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHsmmHMM.bed

rm   wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./'    >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./'      >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./'    >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./'          >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./'     >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./'  >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./'        >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./'       >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed
zcat wgEncodeBroadHmmHuvecHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmHuvecHMM.bed

rm   wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./'    >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./'      >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./'    >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./'          >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./'     >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./'  >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./'        >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./'       >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed
zcat wgEncodeBroadHmmK562HMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmK562HMM.bed

rm   wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./'    >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./'      >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./'    >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./'          >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./'     >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./'  >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./'        >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./'       >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed
zcat wgEncodeBroadHmmNhekHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmNhekHMM.bed

rm wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t1\t0\t\." | sed -e 's/\t1\t0\t\./\t1 Active Promoter\t0\t\./'    >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t2\t0\t\." | sed -e 's/\t2\t0\t\./\t2 Weak Promoter\t0\t\./'      >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t3\t0\t\." | sed -e 's/\t3\t0\t\./\t3 Poised Promoter\t0\t\./'    >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t4\t0\t\." | sed -e 's/\t4\t0\t\./\t4 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t5\t0\t\." | sed -e 's/\t5\t0\t\./\t5 Strong Enhancer\t0\t\./'    >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t6\t0\t\." | sed -e 's/\t6\t0\t\./\t6 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t7\t0\t\." | sed -e 's/\t7\t0\t\./\t7 Weak Enhancer\t0\t\./'      >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t8\t0\t\." | sed -e 's/\t8\t0\t\./\t8 Insulator\t0\t\./'          >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t9\t0\t\." | sed -e 's/\t9\t0\t\./\t9 Txn Transition\t0\t\./'     >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t10\t0\t\." | sed -e 's/\t10\t0\t\./\t10 Txn Elongation\t0\t\./'  >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t11\t0\t\." | sed -e 's/\t11\t0\t\./\t11 Weak Txn\t0\t\./'        >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t12\t0\t\." | sed -e 's/\t12\t0\t\./\t12 Repressed\t0\t\./'       >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t13\t0\t\." | sed -e 's/\t13\t0\t\./\t13 Heterochrom\/lo\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t14\t0\t\." | sed -e 's/\t14\t0\t\./\t14 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed
zcat wgEncodeBroadHmmNhlfHMM.bed.gz | grep -P "\t15\t0\t\." | sed -e 's/\t15\t0\t\./\t15 Repetitive\/CNV\t0\t\./' >> wgEncodeBroadHmmNhlfHMM.bed


wl *.bed
   570580 wgEncodeBroadHmmGm12878HMM.bed
   618287 wgEncodeBroadHmmH1hescHMM.bed
   545647 wgEncodeBroadHmmHepg2HMM.bed
   608568 wgEncodeBroadHmmHmecHMM.bed
   638307 wgEncodeBroadHmmHsmmHMM.bed
   549178 wgEncodeBroadHmmHuvecHMM.bed
   621678 wgEncodeBroadHmmK562HMM.bed
   627623 wgEncodeBroadHmmNhekHMM.bed
   640298 wgEncodeBroadHmmNhlfHMM.bed
All okay

mkdir obsolete
mv wgEncodeBroadHmmGm12878HMM.bed.gz obsolete
mv wgEncodeBroadHmmH1hescHMM.bed.gz obsolete
mv wgEncodeBroadHmmHepg2HMM.bed.gz obsolete
mv wgEncodeBroadHmmHmecHMM.bed.gz obsolete
mv wgEncodeBroadHmmHsmmHMM.bed.gz obsolete
mv wgEncodeBroadHmmHuvecHMM.bed.gz obsolete
mv wgEncodeBroadHmmK562HMM.bed.gz obsolete
mv wgEncodeBroadHmmNhekHMM.bed.gz obsolete
mv wgEncodeBroadHmmNhlfHMM.bed.gz obsolete

sort < wgEncodeBroadHmmGm12878HMM.bed > s_wgEncodeBroadHmmGm12878HMM.bed
sort < wgEncodeBroadHmmH1hescHMM.bed  > s_wgEncodeBroadHmmH1hescHMM.bed
sort < wgEncodeBroadHmmHepg2HMM.bed   > s_wgEncodeBroadHmmHepg2HMM.bed
sort < wgEncodeBroadHmmHmecHMM.bed    > s_wgEncodeBroadHmmHmecHMM.bed
sort < wgEncodeBroadHmmHsmmHMM.bed    > s_wgEncodeBroadHmmHsmmHMM.bed
sort < wgEncodeBroadHmmHuvecHMM.bed   > s_wgEncodeBroadHmmHuvecHMM.bed
sort < wgEncodeBroadHmmK562HMM.bed    > s_wgEncodeBroadHmmK562HMM.bed
sort < wgEncodeBroadHmmNhekHMM.bed    > s_wgEncodeBroadHmmNhekHMM.bed
sort < wgEncodeBroadHmmNhlfHMM.bed    > s_wgEncodeBroadHmmNhlfHMM.bed

mv s_wgEncodeBroadHmmGm12878HMM.bed wgEncodeBroadHmmGm12878HMM.bed
mv s_wgEncodeBroadHmmH1hescHMM.bed  wgEncodeBroadHmmH1hescHMM.bed
mv s_wgEncodeBroadHmmHepg2HMM.bed   wgEncodeBroadHmmHepg2HMM.bed
mv s_wgEncodeBroadHmmHmecHMM.bed    wgEncodeBroadHmmHmecHMM.bed
mv s_wgEncodeBroadHmmHsmmHMM.bed    wgEncodeBroadHmmHsmmHMM.bed
mv s_wgEncodeBroadHmmHuvecHMM.bed   wgEncodeBroadHmmHuvecHMM.bed
mv s_wgEncodeBroadHmmK562HMM.bed    wgEncodeBroadHmmK562HMM.bed
mv s_wgEncodeBroadHmmNhekHMM.bed    wgEncodeBroadHmmNhekHMM.bed
mv s_wgEncodeBroadHmmNhlfHMM.bed    wgEncodeBroadHmmNhlfHMM.bed

wl *.bed
   570580 wgEncodeBroadHmmGm12878HMM.bed
   618287 wgEncodeBroadHmmH1hescHMM.bed
   545647 wgEncodeBroadHmmHepg2HMM.bed
   608568 wgEncodeBroadHmmHmecHMM.bed
   638307 wgEncodeBroadHmmHsmmHMM.bed
   549178 wgEncodeBroadHmmHuvecHMM.bed
   621678 wgEncodeBroadHmmK562HMM.bed
   627623 wgEncodeBroadHmmNhekHMM.bed
   640298 wgEncodeBroadHmmNhlfHMM.bed
All okay

/cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmGm12878HMM_tmp wgEncodeBroadHmmGm12878HMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 
/cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmH1hescHMM_tmp  wgEncodeBroadHmmH1hescHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 
/cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmHepg2HMM_tmp   wgEncodeBroadHmmHepg2HMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 
/cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmHmecHMM_tmp    wgEncodeBroadHmmHmecHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 
/cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmHsmmHMM_tmp    wgEncodeBroadHmmHsmmHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 
/cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmHuvecHMM_tmp   wgEncodeBroadHmmHuvecHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 
/cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmK562HMM_tmp    wgEncodeBroadHmmK562HMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 
/cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmNhekHMM_tmp    wgEncodeBroadHmmNhekHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1 
/cluster/bin/x86_64/hgLoadBed -noNameIx hg18 wgEncodeBroadHmmNhlfHMM_tmp    wgEncodeBroadHmmNhlfHMM.bed -tmpDir=/data/tmp/ -noSort -tab > tryLoad.txt 2>&1

select count(*) from wgEncodeBroadHmmGm12878HMM_tmp;|   570580 |
select count(*) from wgEncodeBroadHmmH1hescHMM_tmp; |   618287 |
select count(*) from wgEncodeBroadHmmHepg2HMM_tmp;  |   545647 |
select count(*) from wgEncodeBroadHmmHmecHMM_tmp;   |   608568 |
select count(*) from wgEncodeBroadHmmHsmmHMM_tmp;   |   638307 |
select count(*) from wgEncodeBroadHmmHuvecHMM_tmp;  |   549178 |
select count(*) from wgEncodeBroadHmmK562HMM_tmp;   |   621678 |
select count(*) from wgEncodeBroadHmmNhekHMM_tmp;   |   627623 |
select count(*) from wgEncodeBroadHmmNhlfHMM_tmp;   |   640298 |

select * from wgEncodeBroadHmmGm12878HMM_tmp limit 1;| 585 | chr1  |          0 |      600 | 15 Repetitive/CNV |     0 | .      |          0 |      600 | 16777215 |
select * from wgEncodeBroadHmmH1hescHMM_tmp limit 1; | 585 | chr1  |          0 |      600 | 15 Repetitive/CNV |     0 | .      |          0 |      600 | 16777215 |
select * from wgEncodeBroadHmmHepg2HMM_tmp limit 1;  | 585 | chr1  |          0 |      400 | 15 Repetitive/CNV |     0 | .      |          0 |      400 | 16777215 |
select * from wgEncodeBroadHmmHmecHMM_tmp limit 1;   | 585 | chr1  |          0 |      600 | 15 Repetitive/CNV |     0 | .      |          0 |      600 | 16777215 |
select * from wgEncodeBroadHmmHsmmHMM_tmp limit 1;   | 585 | chr1  |          0 |      600 | 15 Repetitive/CNV |     0 | .      |          0 |      600 | 16777215 |
select * from wgEncodeBroadHmmHuvecHMM_tmp limit 1;  | 585 | chr1  |          0 |      600 | 15 Repetitive/CNV |     0 | .      |          0 |      600 | 16777215 |
select * from wgEncodeBroadHmmK562HMM_tmp limit 1;   | 585 | chr1  |          0 |      600 | 15 Repetitive/CNV |     0 | .      |          0 |      600 | 16777215 |
select * from wgEncodeBroadHmmNhekHMM_tmp limit 1;   | 585 | chr1  |          0 |      600 | 15 Repetitive/CNV |     0 | .      |          0 |      600 | 16777215 |
select * from wgEncodeBroadHmmNhlfHMM_tmp limit 1;   | 585 | chr1  |          0 |      600 | 15 Repetitive/CNV |     0 | .      |          0 |      600 | 16777215 |

drop table wgEncodeBroadHmmGm12878HMM;
drop table wgEncodeBroadHmmH1hescHMM;
drop table wgEncodeBroadHmmHepg2HMM;
drop table wgEncodeBroadHmmHmecHMM;
drop table wgEncodeBroadHmmHsmmHMM;
drop table wgEncodeBroadHmmHuvecHMM;
drop table wgEncodeBroadHmmK562HMM;
drop table wgEncodeBroadHmmNhekHMM;
drop table wgEncodeBroadHmmNhlfHMM;

rename table wgEncodeBroadHmmGm12878HMM_tmp to wgEncodeBroadHmmGm12878HMM;
rename table wgEncodeBroadHmmH1hescHMM_tmp  to wgEncodeBroadHmmH1hescHMM;
rename table wgEncodeBroadHmmHepg2HMM_tmp   to wgEncodeBroadHmmHepg2HMM;
rename table wgEncodeBroadHmmHmecHMM_tmp    to wgEncodeBroadHmmHmecHMM;
rename table wgEncodeBroadHmmHsmmHMM_tmp    to wgEncodeBroadHmmHsmmHMM;
rename table wgEncodeBroadHmmHuvecHMM_tmp   to wgEncodeBroadHmmHuvecHMM;
rename table wgEncodeBroadHmmK562HMM_tmp    to wgEncodeBroadHmmK562HMM;
rename table wgEncodeBroadHmmNhekHMM_tmp    to wgEncodeBroadHmmNhekHMM;
rename table wgEncodeBroadHmmNhlfHMM_tmp    to wgEncodeBroadHmmNhlfHMM;
show tables like "wgEncodeBroadHmm%";
| wgEncodeBroadHmmGm12878HMM         | 
| wgEncodeBroadHmmH1hescHMM          | 
| wgEncodeBroadHmmHepg2HMM           | 
| wgEncodeBroadHmmHmecHMM            | 
| wgEncodeBroadHmmHsmmHMM            | 
| wgEncodeBroadHmmHuvecHMM           | 
| wgEncodeBroadHmmK562HMM            | 
| wgEncodeBroadHmmNhekHMM            | 
| wgEncodeBroadHmmNhlfHMM            | 
select count(*) from wgEncodeBroadHmmGm12878HMM;|   570580 |
select count(*) from wgEncodeBroadHmmH1hescHMM; |   618287 |
select count(*) from wgEncodeBroadHmmHepg2HMM;  |   545647 |
select count(*) from wgEncodeBroadHmmHmecHMM;   |   608568 |
select count(*) from wgEncodeBroadHmmHsmmHMM;   |   638307 |
select count(*) from wgEncodeBroadHmmHuvecHMM;  |   549178 |
select count(*) from wgEncodeBroadHmmK562HMM;   |   621678 |
select count(*) from wgEncodeBroadHmmNhekHMM;   |   627623 |
select count(*) from wgEncodeBroadHmmNhlfHMM;   |   640298 |

gzip wgEncodeBroadHmmGm12878HMM.bed
gzip wgEncodeBroadHmmH1hescHMM.bed
gzip wgEncodeBroadHmmHepg2HMM.bed
gzip wgEncodeBroadHmmHmecHMM.bed
gzip wgEncodeBroadHmmHsmmHMM.bed
gzip wgEncodeBroadHmmHuvecHMM.bed
gzip wgEncodeBroadHmmK562HMM.bed
gzip wgEncodeBroadHmmNhekHMM.bed
gzip wgEncodeBroadHmmNhlfHMM.bed

# looks good in browser
# files are okay

2011-01-31 Swap out bigWigs that Brian update to version 4
==========================================================
cd /hive/users/braney/bigWigConvert.wgEncodeBroadHistone
ls -1 *.bigWig | wl  151
cd {downLoads}/wgEncodeBroadHistone
ls -1 *.bigWig | wl  151
mv *.bigWig ../obsolete/wgEncodeBroadHistone

cd /hive/users/braney/bigWigConvert.wgEncodeBroadHistone
mv wgEncodeBroadHistoneGm12878ControlStdSig.bigWig.new.bigWig      /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig
mv wgEncodeBroadHistoneGm12878CtcfStdSig.bigWig.new.bigWig         /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878CtcfStdSig.bigWig
mv wgEncodeBroadHistoneGm12878H2azStdSig.bigWig.new.bigWig         /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H2azStdSig.bigWig
mv wgEncodeBroadHistoneGm12878H3k27acStdSig.bigWig.new.bigWig      /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27acStdSig.bigWig
mv wgEncodeBroadHistoneGm12878H3k27me3StdSig.bigWig.new.bigWig     /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27me3StdSig.bigWig
mv wgEncodeBroadHistoneGm12878H3k36me3StdSig.bigWig.new.bigWig     /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k36me3StdSig.bigWig
...
cd {downLoads}/wgEncodeBroadHistone
ls -1 *.bigWig | wl  151
cd release1/
ls -1 *.bigWig | wl  151
# These are links to obsolete bigWigs
rm *.bigWig
ls ../*.bigWig .
ls -1 *.bigWig | wl  151

# Check that bigWigs work in browser.  This will check that /gbdb/hg19/bbi link is okay too
AOKAY

# check metadata by building index.html
../
encodeDownloadsPage.pl -db=hg19 index.html
1251 files all with metadata.  # 1251 file in hgFileUi too
encodeDownloadsPage.pl -db=hg19 -checksum index.html &

2011-02-07 Change white items to ??
===================================
Currently:
1  255,0,0     #FF0000
2  255,105,105 #FF6969
3  207,11,198  #CF0BC6
4  250,202,0   #FACA00 
5  250,202,0   #FACA00
6  255,252,4   #FFFC04
7  255,252,4   #FFFC04
8  10,190,254  #0ABEFE  704254
9  0,176,80    #00B050
10 0,176,80    #00B050
11 153,255,102 #99FF66
12 127,127,127 #7F7F7F
13 255,255,255 #FFFFFF  => #F5F5F5 16119285
14 255,255,255 #FFFFFF  => #D3D3D3 13882323
15 255,255,255 #FFFFFF  => #DCDCDC 14474460

select count(*) from wgEncodeBroadHmmNhlfHMM where reserved = 16777215;|   103835 | 
update wgEncodeBroadHmmGm12878HMM set reserved = 16119285 where reserved = 16777215;
Rows matched: 88467  Changed: 88467  Warnings: 0
update wgEncodeBroadHmmH1hescHMM  set reserved = 16119285 where reserved = 16777215;
Rows matched: 96621  Changed: 96621  Warnings: 0
update wgEncodeBroadHmmHepg2HMM   set reserved = 16119285 where reserved = 16777215;
Rows matched: 84990  Changed: 84990  Warnings: 0
update wgEncodeBroadHmmHmecHMM    set reserved = 16119285 where reserved = 16777215;
Rows matched: 90848  Changed: 90848  Warnings: 0
update wgEncodeBroadHmmHsmmHMM    set reserved = 16119285 where reserved = 16777215;
Rows matched: 87160  Changed: 87160  Warnings: 0
update wgEncodeBroadHmmHuvecHMM   set reserved = 16119285 where reserved = 16777215;
Rows matched: 90766  Changed: 90766  Warnings: 0
update wgEncodeBroadHmmK562HMM    set reserved = 16119285 where reserved = 16777215;
Rows matched: 93219  Changed: 93219  Warnings: 0
update wgEncodeBroadHmmNhekHMM    set reserved = 16119285 where reserved = 16777215;
Rows matched: 92707  Changed: 92707  Warnings: 0
update wgEncodeBroadHmmNhlfHMM set reserved = 16119285 where reserved = 16777215;
Rows matched: 103835  Changed: 103835  Warnings: 0

2011-02-10 Preparing for Release of HMM
=======================================
Got description and added them.
## No restrictions on this data so will remove this setting.
select * from metaDb_tdreszer where obj like "WgEncodeBroadHmm%" and var = "dateUnrestricted";
| wgEncodeBroadHmmGm12878HMM | dateUnrestricted | txt     | 2011-10-21 | 
| wgEncodeBroadHmmH1hescHMM  | dateUnrestricted | txt     | 2011-10-21 | 
| wgEncodeBroadHmmHepg2HMM   | dateUnrestricted | txt     | 2011-10-21 | 
| wgEncodeBroadHmmHmecHMM    | dateUnrestricted | txt     | 2011-10-21 | 
| wgEncodeBroadHmmHsmmHMM    | dateUnrestricted | txt     | 2011-10-21 | 
| wgEncodeBroadHmmHuvecHMM   | dateUnrestricted | txt     | 2011-10-21 | 
| wgEncodeBroadHmmK562HMM    | dateUnrestricted | txt     | 2011-10-21 | 
| wgEncodeBroadHmmNhekHMM    | dateUnrestricted | txt     | 2011-10-21 | 
| wgEncodeBroadHmmNhlfHMM    | dateUnrestricted | txt     | 2011-10-21 | 
update metaDb_tdreszer set val = "2011-01-21" where obj like "WgEncodeBroadHmm%" and var = "dateUnrestricted"; # date submitted
# Perhaps could remove this, but I don't want any unexpected stuff happening.  I found that the calculated date shows up in hgTrackUi!

cd (downloads)/wgEncodeBroadHmm
encodeDownloadsPage.pl -checksum index.html
mkdir release1
cd release1/
cp ../index.html .
cp ../files.txt .
cp ../md5sum.txt .
ln ../*.gz .
ll ../ | grep -v \.gz$ | grep -v \.html | grep -v \.txt 
# Nothing missing
ls -1 | wl  
12 # expect 9 + 3 = 12
cd ..
~/bin/scripts/encodeMkChangeNotes hg18 release1 - > release1/wgEncodeBroadHmm.release1.notes
cp release1/wgEncodeBroadHmm.release1.notes ~/kent/src/hg/makeDb/doc/encodeDccHg18/ 

/cluster/data/encode/pipeline/bin/encodeStatus.pl 3446 approved

# to be done:
/cluster/data/encode/pipeline/bin/encodeStatus.pl 3446 reviewing

2011-04-20 Experimentify
========================
cd trackDb/human/hg18/metaDb/alpha
mdbPrint hg18 -composite=%BroadCh% -experimentify > tmp.txt

mdbUpdate hg18 -composite=%BroadCh% -encodeExp=std -test               
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeBroadChipSeq' has 93 recognizable experiments with 0 missing an expId.
   objects/experiment: min:5  max:6  mean:5.903226.
Found 549 of 550 object(s) would have their experiment ID updated.

mdbUpdate hg18 -composite=%BroadCh% -encodeExp=std
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeBroadHistone' has 93 recognizable experiments with 93 missing an expId.
   objects/experiment: min:3  max:8  mean:6.158940.
Affected 549 row(s) in hg18.metaDb_tdreszer

mdbUpdate hg18 -composite=%BroadCh% -encodeExp=std -accession
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeBroadChipSeq' has 93 recognizable experiments with 0 missing an expId.
   objects/experiment: min:5  max:6  mean:5.903226.
Affected 549 row(s) in hg18.metaDb_tdreszer

mdbPrint hg18 -composite=wgEncodeBroadChipSeq > wgEncodeBroadChipSeq.ra
Using table named 'hg18.metaDb_tdreszer'.
objects:550  vars:11162

gold, gadd, gci, gup,gpush

mdbPrint hg18 -composite=%BroadHmm -experimentify > tmp.txt
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
objects:10  vars:138

mdbUpdate hg18 -composite=%BroadHmm -encodeExp=std -test               
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeBroadHmm' has 9 recognizable experiments with 9 missing an expId.
   objects/experiment: min:1  max:1  mean:1.000000.
Found 9 of 10 object(s) would have their experiment ID updated.
Command would affected 9 row(s) in hg18.metaDb_tdreszer

mdbUpdate hg18 -composite=%BroadHmm -encodeExp=std
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeBroadHmm' has 9 recognizable experiments with 9 missing an expId.
   objects/experiment: min:1  max:1  mean:1.000000.
Affected 9 row(s) in hg18.metaDb_tdreszer

mdbUpdate hg18 -composite=%BroadHmm -encodeExp=std -accession -test
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeBroadHmm' has 9 recognizable experiments with 0 missing an expId.
   objects/experiment: min:1  max:1  mean:1.000000.
Found 9 of 10 object(s) would have their experiment ID updated.
Command would affected 9 row(s) in hg18.metaDb_tdreszer

mdbUpdate hg18 -composite=%BroadHmm -encodeExp=std -accession
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeBroadHmm' has 9 recognizable experiments with 0 missing an expId.
   objects/experiment: min:1  max:1  mean:1.000000.
Affected 9 row(s) in hg18.metaDb_tdreszer

mdbPrint hg18 -composite=wgEncodeBroadHmm > wgEncodeBroadHmm.ra
Using table named 'hg18.metaDb_tdreszer'.
objects:10  vars:156

gold wgEncodeBroadHmm.ra

gold, gadd, gci, gup,gpush

cd {downloads}/wgEncodeBroadChipSeq
encodeDownloadsPage.pl -db=hg18 index.html

cd {downloads}/wgEncodeBroadHmm
encodeDownloadsPage.pl -db=hg18 index.html
cp index.html release1/
cp files.txt release1/
