Description

This track shows the coverage of individual summits processed from Schmittges et al. 2016 from the Hughes lab. ChIP-SEQ of many GFP tagged ZNFs in HEK293 cells. Not all proteins are human, and not all are KRAB-Zinc fingers proteins.

Display Conventions and Configuration

Use in combination with the corresponding summits and meta-summits tracks.

Methods

#make bb summits

mkdir ../hg38reps/schmittges2016

ls ../hg19/schmittges2016/*.bb | cut -f 4 -d "/" | cut -f 1 -d"." | while read i; do bigBedToBed ../hg19/schmittges2016/${i}.bb temp.bed; awk '$4=$1":"$2"-"$3' temp.bed > test.bed; liftOver -multiple test.bed ../lift/hg19_to_hg38reps.over.chain ../hg38reps/schmittges2016/${i}_hg38reps.bed ../hg38reps/schmittges2016/${i}_hg38reps.unmapped; bedSort ../hg38reps/schmittges2016/${i}_hg38reps.bed ../hg38reps/schmittges2016/${i}_hg38reps.bed; bedToBigBed ../hg38reps/schmittges2016/${i}_hg38reps.bed ../hg38reps/hg38reps.sizes ../hg38reps/schmittges2016/${i}_hg38reps.bb; done

#make coverage

ls ../hg38reps/schmittges2016/*.bed | cut -f 4 -d"/" | cut -f 1 -d"." | while read i; do bedtools genomecov -bg -split -i ../hg38reps/schmittges2016/${i}.bed -g ../hg38reps/hg38reps.sizes > temp.bg; bedGraphToBigWig temp.bg ../hg38reps/hg38reps.sizes ../hg38reps/schmittges2016/${i}.bw; done

References

Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T et al. Multiparameter functional diversity of human C2H2 zinc finger proteins. Genome Res. 2016 Dec;26(12):1742-1752. PMID: 27852650; PMC: PMC5131825

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