This track shows the mappings data processed from the ENCODE_TFBS_Summits track. 340 factors, 129 cell types.
This track represents the coverage of individual genomic summits to the Repeat Browser. hg38 coordinates populate the name field. Use in combination with the corresponding meta summits and summit mapping tracks. This composite track has MANY subtracks, please only turn a few on at a time to avoid crashing the browser.
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegDnaseClustered/wgEncodeRegDnaseClusteredV3.bed.gz
gunzip wgEncodeRegDnaseClusteredV3.bed.gz
sed "s/\//-/g" encRegTfbsClusteredWithCells.hg38.bed | awk '{split ($6,a,","); for (i in a) { print ($1"\t"$2"\t"$3"\t"$4"\t"$5"\t+") >> "../hg19/encRegTfbsClustered/encRegTfbsClusteredWithCells_"$4"_"a[i]".bed"}}'
#make bb summits
mkdir ../hg38reps/encRegTfbsClustered
ls ../hg38/encRegTfbsClustered/*.bed | cut -f 4 -d "/" | cut -f 1 -d"." | while read i; do awk '$4=$1":"$2"-"$3' ../hg38/encRegTfbsClustered/*${i}.bed > test.bed; liftOver -multiple test.bed ../lift/hg38_to_hg38reps.over.chain ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bed ../hg38reps/encRegTfbsClustered/${i}_hg38reps.unmapped; bedSort ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bed ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bed; bedToBigBed ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bed ../hg38reps/hg38reps.sizes ../hg38reps/encRegTfbsClustered/${i}_hg38reps.bb; done
#make coverage
ls ../hg38reps/encRegTfbsClustered/*.bed | cut -f 4 -d"/" | cut -f 1 -d"." | while read i; do bedtools genomecov -bg -split -i ../hg38reps/encRegTfbsClustered/${i}.bed -g ../hg38reps/hg38reps.sizes > temp.bg; bedGraphToBigWig temp.bg ../hg38reps/hg38reps.sizes ../hg38reps/encRegTfbsClustered/${i}.bw; done
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Email max@soe.ucsc.edu or markd@ucsc.edu