This track shows the coverage of summits processed from Theunissen et al. 2016, exploring the naive and primed human ES states.
These states have characteristic repeat expression patterns.
Two Chip-Seq assays were done, one for Kap1 and the other one for the H3K9me3 chromatin mark.
Use in combination with the corresponding meta summit and instance mapping tracks.
ls ../hg19/theunissen2016/*.bb | cut -f 4 -d "/" | cut -f 1 -d"." | while read i; do bigBedToBed ../hg19/theunissen2016/${i}.bb temp.bed; awk '$4=$1":"$2"-"$3' temp.bed > test.bed; liftOver -multiple test.bed ../lift/hg19_to_hg38reps.over.chain ../hg38reps/theunissen2016/${i}_hg38reps.bed ../hg38reps/theunissen2016/${i}_hg38reps.unmapped; bedSort ../hg38reps/theunissen2016/${i}_hg38reps.bed ../hg38reps/theunissen2016/${i}_hg38reps.bed; bedToBigBed ../hg38reps/theunissen2016/${i}_hg38reps.bed ../hg38reps/hg38reps.sizes ../hg38reps/theunissen2016/${i}_hg38reps.bb; done
#make coverage
ls ../hg38reps/theunissen2016/*.bed | cut -f 4 -d"/" | cut -f 1 -d"." | while read i; do bedtools genomecov -bg -split -i ../hg38reps/theunissen2016/${i}.bed -g ../hg38reps/hg38reps.sizes > temp.bg; bedGraphToBigWig temp.bg ../hg38reps/hg38reps.sizes ../hg38reps/theunissen2016/${i}.bw; done
Theunissen et al., Cell Stem Cell, 2016
Email max@soe.ucsc.edu or jferna10@ucsc.edu