Overlapping Peaks (Genomic Regions From Chip Seq Expt)

Question

[Dataminer]

Hi!

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

Answer 1

[Vikas Bansal]

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)