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).