Question

Overlapping Peaks And Distance Between Them....

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13.5 years ago

Dataminer ★ 2.8k

Hi!

Consider, you have two peak files A and B.Also you have an intersection file of A and B, say intersect AB (containing overlapping peaks).

Now, how can one know about the distance between overlapping peaks?

Any suggestions?

Thank you.

chip-seq • 4.6k views

ADD COMMENT • link updated 5.4 years ago by Biostar 20 • written 13.5 years ago by Dataminer ★ 2.8k

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Could you please specify what you mean by "peak file": what is the information that is stored in your file?

ADD REPLY • link 13.5 years ago by Istvan Albert 101k

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Well I guess you are the one who down voted my question.... anyways, Peak files are the files containing the genomic regions where T.F. binds to DNA (possibly) these are generated by tools like MACS and are essential part of data analysis of ChIP-ChIP and ChIP-seq. I guess I have cleared your doubt on peak files.... so now could you remove your down vote ?????????????

ADD REPLY • link 13.5 years ago by Dataminer ★ 2.8k

score 2 · Answer 1 · 2012-04-12

May be its late to reply, but while using intersectBed you can specify the percentage of overlap threshold using the parameter '-f'

intersectBed -u -a a.bed -b b.bed -f 0.5

I mostly use a threshold of 0.5 which means any overlap b/w 50-100%, it will be reported. You would need to make a perl/python script to calculate the difference b/w the start/end or better the summits of the overlapping peaks to get a tentative list of the distance for each peak.

Cheers