distance between chip peaks and individual TSS

Question

[Tejaswini]

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?

[Darked89]

you may try: bedtools closest -D a -a my_tss.bed -b my_peaks.bed > result.tsv

Last column will have a distance relative to the TSS. Minus means upstream. You will need to do some filtering based on that

Answer 1

[Alex Reynolds]

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.