Description

This track shows the coverage of individual summits from Imbeault et al 2017. This study was a large scale ChIP-SEQ "screen" of ~200 KRAB Zinc Finger proteins HA tagged and expressed in 293 cells.

Use in combination with the corresponding coverage and instance mapping tracks.

Methods

#make bb summits

mkdir ../hg38reps/imbeault2017

ls ../hg19/imbeault2017/*.bed | cut -f 4 -d "/" | cut -f 1 -d"." | while read i; do awk '$4=$1":"$2"-"$3' ../hg19/imbeault2017/*${i}.bed > test.bed; liftOver -multiple test.bed ../lift/hg19_to_hg38reps.over.chain ../hg38reps/imbeault2017/${i}_hg38reps.bed ../hg38reps/imbeault2017/${i}_hg38reps.unmapped; bedSort ../hg38reps/imbeault2017/${i}_hg38reps.bed ../hg38reps/imbeault2017/${i}_hg38reps.bed; bedToBigBed ../hg38reps/imbeault2017/${i}_hg38reps.bed ../hg38reps/hg38reps.sizes ../hg38reps/imbeault2017/${i}_hg38reps.bb; done

#make coverage

ls ../hg38reps/imbeault2017/*.bed | cut -f 4 -d"/" | cut -f 1 -d"." | while read i; do bedtools genomecov -bg -split -i ../hg38reps/imbeault2017/${i}.bed -g ../hg38reps/hg38reps.sizes > temp.bg; bedGraphToBigWig temp.bg ../hg38reps/hg38reps.sizes ../hg38reps/imbeault2017/${i}.bw; done

References

Imbeault M1, Helleboid PY1, Trono D1.

Nature. 2017 Mar 23;543(7646):550-554. doi: 10.1038/nature21683. Epub 2017 Mar 8.

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