Question: Overlapping Peaks (Genomic Regions From Chip Seq Expt)
gravatar for Dataminer
7.0 years ago by
Dataminer2.6k wrote:


I have a set of peaks say set A (containing 500 genomic regions) and I also have two more set of peaks peaks say B1 and B2 (containing 700 and 2000 genomic regions respectively).

What I want to know if the genomic regions in set A are present in set B1 or/and B2?

An answer like this:

Set A SetB1 Set B2

peak1 Yes No

Peak2 yes yes

where peak1/peak2 are genomic co-ordinates(chr chrstart chrstop).

Thank you

ADD COMMENTlink modified 7.0 years ago by Vikas Bansal2.3k • written 7.0 years ago by Dataminer2.6k
gravatar for Vikas Bansal
7.0 years ago by
Vikas Bansal2.3k
Berlin, Germany
Vikas Bansal2.3k wrote:

Use BEDtools intersect. something like this-

intersectBed -a A.file  -b B1.file -wb # wb will give you fields from file B1.file, use -v option if you want to know that are not present in file B1.file
intersectBed -a A.file  -b B2.file -wb 
#now manipulate the output files (may be using perl script) to convert in yes or no (in terms of overlapping and non overlapping)
ADD COMMENTlink written 7.0 years ago by Vikas Bansal2.3k
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