    mkdir /hive/groups/encode/dcc/data/HudsonAlphaMethyl27
    cd /hive/groups/encode/dcc/data/HudsonAlphaMethyl27

    cp /cluster/home/tingwang/ENCODE/Methyl27/ENCODE_methyl27.txt .
    cp /cluster/home/tingwang/ENCODE/script/methyl27_1.pl .

# 2009-08-04 braney, changed red to orange for methylated calls
    ./methyl27_1.pl ENCODE_methyl27.txt
    
    for i in *.bed
    do
	f=`basename $i .bed`
	hgLoadBed hg18 $f $i
    done

    for i in *.bed
    do
	gzip $i
    done

    mkdir /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeHudsonalphaMethyl27
    for i in *.bed.gz
    do
	rm -f /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeHudsonalphaMethyl27/$i

	ln -s `pwd`/$i /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeHudsonalphaMethyl27
    done








