This track shows the mappings data processed from the UW hg19 Genome Browser track. Many cell types and histone marks are included here.
This track represents the mappings 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.
rsync -a -P rsync://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwHistone/*broadPeak* ./
ls | while read i; do awk -v OFS="\t" '{if ($8 > 10){print $1,$2,$3, "peak_"NR, $5, $6}}' $i > temp.bed; cat temp.bed > $i; done
ls | while read i; do awk '$4=$1":"$2"-"$3' $i > test.bed; liftOver -multiple test.bed ../../lift/hg19_to_hg38reps.over.chain ../../hg38reps/wgEncodeUwHistone/${i}_hg38reps.bed ../../hg38reps/wgEncodeUwHistone/${i}_hg38reps.unmapped; bedSort ../../hg38reps/wgEncodeUwHistone/${i}_hg38reps.bed ../../hg38reps/wgEncodeUwHistone/${i}_hg38reps.bed; bedToBigBed ../../hg38reps/wgEncodeUwHistone/${i}_hg38reps.bed ../../hg38reps/hg38reps.sizes ../../hg38reps/wgEncodeUwHistone/${i}_hg38reps.bb; done
ls *.bed | cut -f 1 -d"." | while read i; do bedtools genomecov -bg -split -i ${i}.bed -g ../../hg38reps/hg38reps.sizes > temp.bg; bedGraphToBigWig temp.bg ../../hg38reps/hg38reps.sizes ${i}.bw; done
Email max@soe.ucsc.edu or jferna10@ucsc.edu