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For Gemini: Create a master ChromHMM track from the 9 distinct cell types.
echo "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmGm12878HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmH1hescHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHepg2HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHmecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHsmmHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHuvecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmK562HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhekHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhlfHMM.bed.gz" \
> chromhmm-files.txt
# downlaod
for remote in `cat chromhmm-files.txt`
do
wget $remote
done
# uncompress
for zip in `ls *.gz`
do
gunzip -f $zip
done
# bed+ -> ~bedgraph
for bed in `ls *.bed`
do
cut -f 1-4 $bed > $bed.bedg
done
# union of all intervals across all 9 cell types
bedtools unionbedg -i *.bedg > master.chromhmm.bedg
Owner

arq5x commented Jul 18, 2012

Remember to tweak the labels for the master bedg. Perhaps some add'l massaging of the values before making it to gemini.

brentp commented Jun 11, 2013

set -ex
cell_types=(Gm12878 H1hesc Hepg2 Hmec Hsmm Huvec K562 Nhek Nhlf)
dir=chromHMM

mkdir -p $dir; cd $dir;

for ct in "${cell_types[@]}"; do
    echo $ct;
    remote=http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmm${ct}HMM.bed.gz
    F=$(basename $remote .gz)
    wget --quiet -O - $remote | zcat - | cut -f 1-4 | perl -pe 's/\d+_(.+)/$1/' > $F
done

bedtools unionbedg -header -names "${cell_types[@]}" -i *.bed > master.chromhmm.bedg
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