Question: Bedtools intersect with minimum overlap required as a number
gravatar for AmeenS
5.6 years ago by
United States
AmeenS0 wrote:

Hello all.

I have 3 column bed files (chrom, chromStart, chromEnd). I am looking to run bedtools intersect to determine which results are conserved between multiple files.

The constraint is that I want it to only consider overlaps of 20 or more base pairs. All tools in the bedtools suite I have seen only offer to restrict the minimum overlap as a proportion of the first file.

Do any of you know of any tool in the bedtools suite that offers this restriction by quantity instead of proportion, or includes a printout of how much overlap there is, so that I can descriminate the results afterwards?


mapping map intersect bedtools • 3.2k views
ADD COMMENTlink modified 5.6 years ago by PoGibas4.8k • written 5.6 years ago by AmeenS0
gravatar for PoGibas
5.6 years ago by
PoGibas4.8k wrote:

Bedtools intersect -wo does exactly what you want ("write the original A and B entries plus the number of base pairs of overlap"), please read documentation :-/


ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by PoGibas4.8k

Thanks for the help. I read the docoumentation many times, but apparently not closely enough.

ADD REPLYlink written 5.5 years ago by AmeenS0
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