Question: Can Bedtools be used to find features that exist in one bed file, but not in two others?
1
gravatar for Ashley S.
2.8 years ago by
Ashley S.30
Ashley S.30 wrote:

Hi everyone, sorry for the basic nature of this question, but this is something I'm struggling to see how to do properly. I have three BED files, and I'm trying to think of the best way to find regions that are unique to only one of them (i.e., specific regions that exist in that one but not in the two others). I know Bedtools can be used to find features that do not overlap between two BED files using the intersect command and the -v option, but I do think it's working like I want it to when I intersect the original bed file with more than one other.

I'd also like to get a bit broader and find regions that are shared between two of the datasets but not a third, but for now just finding regions specific to only one will be enough, so if anyone has any insight on how best to do this (preferably using BEDtools or something else equally easy for a novice like me), then I'd be very appreciative! Thanks!

bedtools • 885 views
ADD COMMENTlink modified 2.8 years ago by Chris Miller21k • written 2.8 years ago by Ashley S.30
2
gravatar for Chris Miller
2.8 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:
bedtools intersect -a FILE1 -b <(cat FILE2 FILE3 | bedtools sort) -v >OUTFILE
ADD COMMENTlink written 2.8 years ago by Chris Miller21k
1

Thanks! Will try that!

ADD REPLYlink written 2.8 years ago by Ashley S.30
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