# convert Mac => Unix:
tr '\r' '\n' < StanfordChip-FOXP2.DDF.original > StanfordChip-FOXP2.DDF

Q) discrepancies b/n DDF and data directory?

awk '{print $1}' StanfordChip-FOXP2.DDF > 1.txt
remove first line
ls data | awk '{print $1}' | sort > 2.txt
diff 1.txt 2.txt
0a1
> FoxP2_PFSK1_SL102_hg18.TagAlign
6d6
< FoxP2_SK-N-MC_SL102_hg18.TagAlign

Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/Encode.pm line 275.
Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/Encode.pm line 275.
Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/Encode.pm line 304.

add "data/" prefix for all files

change "PSFK-1"  to "PFSK-1" in DDF

Format of narrowPeak file FoxP2_PFSK1_SL13_peakcalls.narrowPeak is invalid (missing many columns).

grep '^newcontam' data/FoxP2_PFSK1_SL16_hg18.TagAlign
data/FoxP2_PFSK1_SL16_hg18.TagAlign
data/FoxP2_SK-N-MC_SL102_hg18.TagAlign

Q) Figure out what are the weird chrom names?

perl -e 'while(<>) {if(/^(\S+)/) {$hash{$1}++;}} print join("\n", sort keys %hash) . "\n";' FoxP2_SK-N-MC_SL102_hg18.TagAlign > uniq.txt &

found 2 odd chrom names:

humRibosomal.fasta
newcontam

egrep -v '^(newcontam|humRibosomal\.fasta)' FoxP2_SK-N-MC_SL102_hg18.TagAlign.original > FoxP2_SK-N-MC_SL102_hg18.TagAlign
egrep -v '^(newcontam|humRibosomal\.fasta)' FoxP2_PFSK1_SL16_hg18.TagAlign.original > FoxP2_PFSK1_SL16_hg18.TagAlign

Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/doEncodeValidate.pl line 742.
Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/doEncodeValidate.pl line 767.
Use of uninitialized value in addition (+) at /cluster/bin/scripts/doEncodeValidate.pl line 769.
Use of uninitialized value in string eq at /cluster/bin/scripts/doEncodeValidate.pl line 776.
Use of uninitialized value in string eq at /cluster/bin/scripts/doEncodeValidate.pl line 776.
  View: RawSignal
Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/doEncodeValidate.pl line 742.
Use of uninitialized value in concatenation (.) or string at /cluster/bin/scripts/doEncodeValidate.pl line 767.
Use of uninitialized value in addition (+) at /cluster/bin/scripts/doEncodeValidate.pl line 769.
Use of uninitialized value in string eq at /cluster/bin/scripts/doEncodeValidate.pl line 776.
Use of uninitialized value in string eq at /cluster/bin/scripts/doEncodeValidate.pl line 776.

caused by MS-DOS text files (ugh).

Q) How big are the files?

One of the control tagAlign files:

wc -l data/FoxP2_PFSK1_SL16_hg18.TagAlign.original
23,550,618

One of the experimental files:

wc -l FoxP2_SK-N-MC_SL144_hg18.TagAlign
13,411,341

Rename the project Rami created:

hgsql encpipeline_prod
update projects set name = 'HudsonAlpha PFSK-1/SK-N-MC Control' where id = 6;

hgLoadBed hg18 HAMethylSeq ~/tmp/methyl.bed -tmpDir=/data/tmp -bedGraph=4
hgLoadBed hg18 HAMethylSeq ~/tmp/HCT116_hpaII.txt.BED -tmpDir=/data/tmp -bedGraph=4

2009-02-10:

Fixed various errors in HudsonAlpha_MethylSeq_Feb0909.DDF (add/subtract tabs etc.)
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/204 >& validate_error &

Orange = methylated; blue = non-methylated

Hypomethylation in HAL, and fetus and BG02ES (but no gene nearby):

chr6:31,247,115-31,267,634

Hypomethylation in human adult liver, and fetus:

chr12:112,685,995-112,696,308

Hypomethylation in human adult liver, and fetus:

chr17:7,584,398-7,586,905

Hypermethylation only in a cancer cell:

chr17:7,548,069-7,550,576

chr12:112,375,893-112,403,444 (LHX5)

Hypermethylation only in late fetus and adult:

chr12:120,130,554-120,135,393

chr1:219,118,454-219,126,339 (HLX, but not near promoter)

/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/204 > upload_error 2>&1 &

2009-02 round:

251, 259-262

TODO:

/hive/groups/encode/dcc/pipeline/encpipeline_prod/251 - figure out how to deal with control; e.g.:

exp_data/Methylseq_GM12878_R1_hpa_1pcr.TagAlign	Alignments	GM12878	1		
exp_data/Methylseq_GM12878_R1_msp_1pcr.TagAlign	Alignments	GM12878	1			

#########################################################################################################
# Deal with loading ftp data after that fact
# 2009
#########################################################################################################

Larry,
I'm currenly sending our fastq files for most of our ChIP-Seq submissions so far:
HudsonAlphaChip_Bg_GM12878_K562         
HudsonAlphaChip_RNAPol2_GM12878_K562         
HudsonAlphaChip_GABP_GM12878_K562         
HudsonAlphaChip_NRSF_GM12878_K562         
HudsonAlphaChip_SRF_GM12878_K562         
HudsonAlphaChip_TAF250_GM12878_Dec08         
HudsonAlphaChip_TAF250_K562_Dec08

Each of the above will be represented by a tar.gz names FASTQ_<Submission Name>. Inside each tar.gz are .fasq files for each of the experiments (uniquely marked by the Library Id - ex: ..._SL242_...fastq).

D FASTQ_HudsonAlphaChip_Bg_GM12878_K562.tar.gz
D FASTQ_HudsonAlphaChip_GABP_GM12878_K562.tar.gz
D FASTQ_HudsonAlphaChip_NRSF_GM12878_K562.tar.gz
D FASTQ_HudsonAlphaChip_RNAPol2_GM12878_K562.tar.gz
D FASTQ_HudsonAlphaChip_SRF_GM12878_K562.tar.gz
W FASTQ_HudsonAlphaChip_TAF250_GM12878_Dec08.tar.gz - only 1 experiment? Gm12878/TafII?
W FASTQ_HudsonAlphaChip_TAF250_K562_Dec08.tar.gz

Each of the above will be represented by a tar.gz names FASTQ_<Submission
Name>. Inside each tar.gz are .fasq files for each of the experiments
(uniquely marked by the Library Id - ex: ..._SL242_...fastq).

"Bg" = control/input

tar tzvf FASTQ_HudsonAlphaChip_NRSF_GM12878_K562.tar.gz
drwxr-xr-x encode/staff      0 2009-01-14 14:56:16 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/
-rw-r--r-- encode/staff 193832511 2009-01-14 14:26:06 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30DMJAAXX_SL202_s_1_sequence.txt.fastq
-rw-r--r-- encode/staff 130633836 2009-01-14 14:32:00 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ENLAAXX_SL221_s_1_sequence.txt.fastq
-rw-r--r-- encode/staff 338440635 2009-01-14 14:32:10 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ENLAAXX_SL221_s_2_sequence.txt.fastq
-rw-r--r-- encode/staff 277341720 2009-01-14 14:32:18 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ENLAAXX_SL221_s_3_sequence.txt.fastq
-rw-r--r-- encode/staff 561864878 2009-01-14 14:32:34 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ENLAAXX_SL221_s_8_sequence.txt.fastq
-rw-r--r-- encode/staff 187817403 2009-01-14 14:26:11 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ET2AAXX_SL202_s_2_sequence.txt.fastq
-rw-r--r-- encode/staff 291247386 2009-01-14 14:32:43 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30ET2AAXX_SL204_s_8_sequence.txt.fastq
-rw-r--r-- encode/staff 715598490 2009-01-14 14:33:04 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/30GJ8AAXX_SL221_s_4_sequence.txt.fastq
-rw-r--r-- encode/staff 196632239 2009-01-14 14:33:09 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204GV_SL204_s_1_sequence.txt.fastq
-rw-r--r-- encode/staff 208102467 2009-01-14 14:33:15 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204GV_SL204_s_2_sequence.txt.fastq
-rw-r--r-- encode/staff 253398035 2009-01-14 14:33:23 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204GV_SL204_s_3_sequence.txt.fastq
-rw-r--r-- encode/staff 356976207 2009-01-14 14:26:22 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204PT_SL202_s_1_sequence.txt.fastq
-rw-r--r-- encode/staff 379577169 2009-01-14 14:26:32 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204PT_SL202_s_2_sequence.txt.fastq
-rw-r--r-- encode/staff 395860545 2009-01-14 14:26:44 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204PT_SL202_s_3_sequence.txt.fastq
-rw-r--r-- encode/staff 395647171 2009-01-14 14:26:55 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC204PT_SL202_s_4_sequence.txt.fastq
-rw-r--r-- encode/staff 361962255 2009-01-14 14:27:05 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209TN_SL202_s_5_sequence.txt.fastq
-rw-r--r-- encode/staff 343422718 2009-01-14 14:33:33 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209TN_SL204_s_7_sequence.txt.fastq
-rw-r--r-- encode/staff 302635377 2009-01-14 14:33:41 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209VL_SL221_s_1_sequence.txt.fastq
-rw-r--r-- encode/staff 424945463 2009-01-14 14:33:54 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209VL_SL221_s_2_sequence.txt.fastq
-rw-r--r-- encode/staff 333914738 2009-01-14 14:34:03 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209VL_SL222_s_3_sequence.txt.fastq
-rw-r--r-- encode/staff 344272962 2009-01-14 14:34:13 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC209VL_SL222_s_4_sequence.txt.fastq
-rw-r--r-- encode/staff 486213829 2009-01-14 14:34:27 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20AJD_SL221_s_4_sequence.txt.fastq
-rw-r--r-- encode/staff 469495268 2009-01-14 14:34:41 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20AJD_SL222_s_5_sequence.txt.fastq
-rw-r--r-- encode/staff 557509406 2009-01-14 14:34:56 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL204_s_3_sequence.txt.fastq
-rw-r--r-- encode/staff 562488011 2009-01-14 14:35:12 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL204_s_4_sequence.txt.fastq
-rw-r--r-- encode/staff 589184958 2009-01-14 14:35:29 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL221_s_5_sequence.txt.fastq
-rw-r--r-- encode/staff 597901196 2009-01-14 14:35:47 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL221_s_6_sequence.txt.fastq
-rw-r--r-- encode/staff 512389254 2009-01-14 14:36:02 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL222_s_7_sequence.txt.fastq
-rw-r--r-- encode/staff 540333106 2009-01-14 14:36:17 FASTQ_HudsonAlphaChip_NRSF_GM12878_K562/FC20ATL_SL222_s_8_sequence.txt.fastq

find . -type f -exec cat {} \; | gzip -c > /cluster/data/encode/pipeline/downloads/wgEncodeHudsonalphaChipSeq/wgEncodeHudsonalphaChipSeqRawSignalRep1Gm12878Control.gz

Sanity checking:

zcat /hive/groups/encode/dcc/analysis/ftp/pipeline/wgEncodeHudsonalphaChipSeq/wgEncodeHudsonalphaChipSeqAlignmentsRep1Gm12878Control.tagAlign.gz | wc -l
14164649 - 14 million

replicate2:

16222442 - 16 million

cd /hive/groups/encode/dcc/pipeline/ftp/prod/rrauch/FASTQ_HudsonAlphaChip_Bg_GM12878_K562
egrep '^@' FC30P52AAXX_SL233_s_7_sequence.txt.fastq | wc -l
5,191,814

5,191,814 * 30 = 155,754,420

That's 155 million reads for both replicates?

They only used 1/10 of the reads?


filename(s)    cell antibody    replicate       control
cat FC20AME_SL217_s_4_sequence.txt.fastq FC20ATK_SL217_s_1_sequence.txt.fastq FC20ATK_SL217_s_2_sequence.txt.fastq FC20ATK_SL217_s_3_sequence.txt.fastq FC20ATK_SL217_s_4_sequence.txt.fastq GM12878 . 1 true
cat 30EMPAAXX_SL218_s_1_sequence.txt.fastq FC20AME_SL218_s_5_sequence.txt.fastq FC20ATK_SL218_s_5_sequence.txt.fastq FC20ATK_SL218_s_6_sequence.txt.fastq FC20ATK_SL218_s_7_sequence.txt.fastq FC20ATK_SL218_s_8_sequence.txt.fastq GM12878 . 2 true
cat 303praaxx_SL233_s_4_sequence.txt.fastq 30DCTAAXX_SL233_s_1_sequence.txt.fastq 30DKKAAXX_SL233_s_5_sequence.txt.fastq 30DLBAAXX_SL233_s_1_sequence.txt.fastq 30EMPAAXX_SL233_s_2_sequence.txt.fastq 30G4WAAXX_SL233_s_3_sequence.txt.fastq 30P07AAXX_SL233_s_4_sequence.txt.fastq FC209VY_SL233_s_4_sequence.txt.fastq FC20E3HAAXX_SL233_s_4_sequence.txt.fastq FC30P52AAXX_SL233_s_3_sequence.txt.fastq FC30P52AAXX_SL233_s_7_sequence.txt.fastq K562 . 1 true
cat 303praaxx_SL234_s_5_sequence.txt.fastq 30DCTAAXX_SL234_s_2_sequence.txt.fastq 30EFCAAXX_SL234_s_1_sequence.txt.fastq 30EFCAAXX_SL234_s_2_sequence.txt.fastq 30EMPAAXX_SL234_s_3_sequence.txt.fastq 30G4WAAXX_SL234_s_4_sequence.txt.fastq FC209VY_SL234_s_5_sequence.txt.fastq FC20E3HAAXX_SL234_s_5_sequence.txt.fastq                                                                                                                          K562 . 2 true

cd /hive/groups/encode/dcc/analysis/ftp/pipeline/wgEncodeHudsonalphaChipSeq
zcat *fastq.gz | wc -l
499097056
cd /hive/groups/encode/dcc/pipeline/ftp/prod/rrauch/FASTQ_HudsonAlphaChip_Bg_GM12878_K562
cat *.fastq | wc -l
499097056

they match (good!)

touch -r wgEncodeHudsonalphaChipSeqAlignmentsPfsk1Control.tagAlign.gz *fastq*

# figure out which files are missing
ls -lt *tagAlign.gz* | perl -ne 's/(RawData|Alignments)//g; if(/(\S+?)\./) { print "$1\n"; }' | sort > tagAlign.txt
ls -lt *fastq.gz* | perl -ne 's/(RawData|Alignments)//g; if(/(\S+?)\./) { print "$1\n"; }' | sort > fastq.txt
diff tagAlign.txt fastq.txt

Q) How do I make sure that Rami didn't screw up and give us non-matching fastq's?

pushd /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeHudsonalphaChipSeq/
~/tmp/faSanityCheck.pl *tagAlign.gz

Couldn't find GAAGTAGTGAGACAGTGAGTTGGAT from wgEncodeHudsonalphaChipSeqAlignmentsRep1K562Tafii.tagAlign.gz in wgEncodeHudsonalphaChipSeqRawDataRep1K562Tafii.fastq.gz

Confirmed by re-running the command.

	/hive/groups/encode/dcc/pipeline/ftp/prod/rrauch/FASTQ_HudsonAlphaChip_TAF250_K562_Dec08
	grep GAAGTAGTGAGACAGTGAGTTGGAT *.fastq

finds nothing (another confirmation).

Is this a TAF-II vs. TAF250 issue?


How about in Yale data?

pushd /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq

Couldn't find TTTATGTTTCTTTTTGTCTTCTCTCTTT from 
         wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz in wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz

With reverse logic:

Couldn't find TACTCTAATCCTTACAGAAAAAAAAAGA from 
         wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz in wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz

         # that is line 38 of wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz
         chr7    49295084        49295112        TCTTTTTTTTTCTGTAAGGATTAGAGTA    1000    -
         # and line 146 of wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz

Therefore, they do NOT put the reverse strand in the tagAlign file.

zcat wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz | more
chr18   28418426        28418454        CAGTCGATTTCCATTATTGAAGTTAGAA    250     +
chr1    81592198        81592226        GGCATGAATCTTTGAGAAGCGTAGCTTT    250     +
chr6    165185914       165185942       CATTTGGATTTCCTGTTATAACAAAAAT    1000    +
chr3    96059483        96059511        AAGGACTCCCTCTTCAATAATTGGTTCT    250     -

I couldn't find line 4, AAGGACTCCCTCTTCAATAATTGGTTCT, its complement or
complement reverse in wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz

However, the first line of the tagAlign, CAGTCGATTTCCATTATTGAAGTTAGAA, is on
line 2 of wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz

zcat wgEncodeYaleChIPseqRawDataGm12878Input.fastq.gz | wc -l
55,835,940 / 4 = 13,958,985

zcat wgEncodeYaleChIPseqAlignmentsGm12878Input.tagAlign.gz | wc -l
11,543,712

zcat wgEncodeYaleChIPseqRawDataRep3Nb4Pol2.fastq.gz | wc -l
19443428 / 4 = 4,860,857

zcat wgEncodeYaleChIPseqAlignmentsRep3Nb4Pol2.tagAlign.gz | wc -l
4,330,530

So, they use almost all of their reads?!? That seems suspicious.

And even more places (UTA):

[larrym@hgwdev wgEncodeChromatinMap]$ ~/kent/src/hg/encode/encodeValidate/tagAlignSanityCheck.pl -reverse wgEncodeUtaChIPseqAlignmentsRep*tagAlign*
Couldn't find the following sequences from wgEncodeUtaChIPseqAlignmentsRep3Gm12878Ctcf.tagAlign.gz in wgEncodeUtaChIPseqRawDataRep3Gm12878Ctcf.fastq.gz
AAGCATGGTGGCATGCGCATGTGGTCCCAGANC

But maybe that's b/c it's not reversed

2009-04-03

Rami uploaded PFSK-1 and SK-N-MC replicates 1 and 2 and control - 

cd /hive/groups/encode/dcc/pipeline/ftp/prod/rrauch
tar xzvf HudsonAlpha_PFSK-1_SK-N-MC_FOXP2_FASTQ.tar.gz
cd PFSK-1_SK-N-MC_FOXP2_FASTQ

~/tmp/ramiDdf.pl < ~/tmp/fpsk.ddf

generated wgEncodeHudsonalphaChipSeqRawDataRep2SknmcFoxp2.fastq.gz and wgEncodeHudsonalphaChipSeqRawDataRep2Pfsk1Foxp2.fastq.gz

~/kent/src/hg/encode/encodeValidate/tagAlignSanityCheck.pl *Rep2SknmcFoxp2.tagAlign.gz *Rep2Pfsk1Foxp2.tagAlign.gz
wgEncodeHudsonalphaChipSeqAlignmentsRep2SknmcFoxp2.tagAlign.gz is ok

Couldn't find the following sequences from wgEncodeHudsonalphaChipSeqAlignmentsRep2Pfsk1Foxp2.tagAlign.gz in wgEncodeHudsonalphaChipSeqRawDataRep2Pfsk1Foxp2.fastq.gz
CATTTTACAGATGGAGAAACAGATT
ACTTACAGTCATGGCACAAGGGGAA
CTCATGTCAACGTTAAAAATGCTGT
GAACCAGGTGTGAACTGGTGTCTAG
AGTCCTGAGAATTCTACATCTCACG
TTTGTAACGACAGGGTCTTGCTATG

(6 out of 10).

Still missing replicate 1 for FOXP2 in PFSK-1 and SK-N-MC!

#########################################################################################################
# Put whatever we can into the pushQ
# 2009-04-23
#########################################################################################################

pushQ items that are ready:

releaseLogUrl = http://genome.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeHudsonalphaChipseq

# this are still missing fastqs (PFSK-1, SK-N-MC data)
6 -> 004635
7 -> 004636

# these are ready
52 -> 004636
51 -> 004637
67 -> 004638
70 -> 004639
71 -> 004640
125 -> 004641
126 -> 004642

all seven have been consolidated into: 004636

2009-09-22 Tim is taking over!
==============================
select id,name,status,user_id from projects where user_id = 8;
+-----+----------------------------------------------------+-----------------+---------+
| id  | name                                               | status          | user_id |
+-----+----------------------------------------------------+-----------------+---------+
|   6 | HudsonAlpha PFSK-1/SK-N-MC Control                 | approved        |       8 | 
|   7 | HudsonAlpha PFSK-1/SK-N-MC FOXP2                   | approved        |       8 | 
|  51 | HudsonAlphaChip_Bg_GM12878_K562                    | released        |       8 | 
|  52 | HudsonAlphaChip_RNAPol2_GM12878_K562               | released        |       8 | 
|  67 | HudsonAlphaChip_GABP_GM12878_K562                  | released        |       8 | 
|  70 | HudsonAlphaChip_NRSF_GM12878_K562                  | released        |       8 | 
|  71 | HudsonAlphaChip_SRF_GM12878_K562                   | released        |       8 | 
| 103 | HudsonAlpha_Genotype_K562_GM12878_HepG2            | validate failed |       8 | 
| 125 | HudsonAlphaChip_TAF250_GM12878_Dec08               | released        |       8 | 
| 126 | HudsonAlphaChip_TAF250_K562_Dec08                  | released        |       8 | 
| 204 | HudsonAlpha_Methyl_Seq_Feb0909                     | approved        |       8 | 
| 259 | HudsonAlpha_ChIPSeq_Sin3Ak-20_K562_GM12878_Feb2709 | displayed       |       8 | 
| 260 | HudsonAlpha_ChIPSeq_Egr-1_K562_GM12878_Feb2709     | displayed       |       8 | 
| 261 | HudsonAlpha_ChIPSeq_USF-1_K562_GM12878_Feb2709     | displayed       |       8 | 
| 262 | HudsonAlpha_ChIPSeq_CONTROL_K562_GM12878_Feb2709   | displayed       |       8 | 
| 268 | HudsonAlpha_ChIP-Seq-FEB09_FASTQ                   | loaded          |       8 | 
| 387 | HudsonAlpha_MethylSeq_K562_GM12878_Mar09           | displayed       |       8 | 
| 419 | HudsonAlpha_HepG2_Jul-09_FASTQ                     | validate failed |       8 | 
| 422 | HudsonAlpha_GM12878_Jul-09                         | displayed       |       8 | 
| 432 | HudsonAlpha_HepG2_Jul-09                           | displayed       |       8 | 
| 433 | HudsonAlpha_HeLa_Jul-09                            | displayed       |       8 | 
| 434 | HudsonAlpha_U87_Jul-09                             | displayed       |       8 | 
| 435 | HudsonAlpha_PANC1_Jul-09                           | displayed       |       8 | 
| 436 | HudsonAlpha_PFSK1_Jul-09                           | displayed       |       8 | 
| 437 | HudsonAlpha_BE2C_Jul-09                            | displayed       |       8 | 
| 438 | HudsonAlpha_HTB11_Jul-09                           | displayed       |       8 | 
+-----+----------------------------------------------------+-----------------+---------+
26 rows in set (0.00 sec)

Not to bad.  Why 2 validate failed?

It appears that:
1) no signals are provided.  
2) We generate Raw Signals for ChIPseq
3) fastq are provided separately for ChIPseq.
4) Replicates go all the way up to the top: ChIPseq:peaks, MethylSeq:regions
5) Only Regions are displayed in MethylSeq
6) No Methyl27 submission.  Track seems to be hand loaded.
7) Dir 103 is CNV which also seems to have been hand loaded and is owned by Brian.

