distance between chip peaks and individual TSS
I have generated my peak data through chip sequencing data and I have individual transcription sites coordinates from RNA sequencing data. How to compare the distance between these TSS and peaks, so that I can find the closest TSS to peak and observe if there is any change in transcription between the control and treated?
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Alex Reynolds
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Tejaswini •
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Tejaswini •
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Via BEDOPS closest-features:
$ closest-features --closest --dist positions.bed TSS.bed > answer.bed
You could use awk or Python (for example) to chop up answer.bed by condition or generate distance distribution plots, etc.
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you may try:
bedtools closest -D a -a my_tss.bed -b my_peaks.bed > result.tsvLast column will have a distance relative to the TSS. Minus means upstream. You will need to do some filtering based on that