Description

This track shows the mappings data processed from the UW hg19 Genome Browser track. Many cell types and histone marks are included here.

Display Conventions and Configuration

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.

Methods

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

References

Email max@soe.ucsc.edu or jferna10@ucsc.edu