Description

This track shows the coverage of individual summits from a large scale ChIP-SEQ study described in Tsankov et al., "Transcription factor binding dynamics during human ES cell differentiation", Nature 2015. In this work, the authors performed ~38 ChIP-SEQ of transcription factors in stem cells at different stages of differentiation (pluripotent state, endodem, mesoendoderm, etc).

Display Conventions and Configuration

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

Methods

#make summits

ls ../hg19/tsankov2014/*.bb | cut -f 4 -d "/" | cut -f 1 -d"." | while read i; do bigBedToBed ../hg19/tsankov2014/${i}.bb temp.bed; awk '$4=$1":"$2"-"$3' temp.bed > test.bed; liftOver -multiple test.bed ../lift/hg19_to_hg38reps.over.chain ../hg38reps/tsankov2014/${i}_hg38reps.bed ../hg38reps/tsankov2014/${i}_hg38reps.unmapped; bedSort ../hg38reps/tsankov2014/${i}_hg38reps.bed ../hg38reps/tsankov2014/${i}_hg38reps.bed; bedToBigBed ../hg38reps/tsankov2014/${i}_hg38reps.bed ../hg38reps/hg38reps.sizes ../hg38reps/tsankov2014/${i}_hg38reps.bb; done

#make coverage

ls ../hg38reps/tsankov2014/*.bed | cut -f 4 -d"/" | cut -f 1 -d"." | while read i; do bedtools genomecov -bg -split -i ../hg38reps/tsankov2014/${i}.bed -g ../hg38reps/hg38reps.sizes > temp.bg; bedGraphToBigWig temp.bg ../hg38reps/hg38reps.sizes ../hg38reps/tsankov2014/${i}.bw; done

References

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