Hi guys. I have two peak files. One is from ATAC seq and the other is from H3K27ac chip seq. I am trying to merge these two peaks files together and get a file with overlapping peaks. There are several questions that I have here:
what scripts or programs are good for that application? (bedops and bedmap?)
I used MACS2 to call peaks: regular peaks calling for ATAC seq and broad peaks calling for H3K27ac chip seq. I am concerned whether the different peak calling methods will influence the overlapping results. Thank you!