Description

This track shows the summits processed and mapped to the Repeat Browserfrom 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.

Display Conventions and Configuration

Use in combination with the corresponding meta summit and coverage tracks.

Methods

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

References

Theunissen et al., Cell Stem Cell, 2016

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