detect similiar/different peaks from two samples

[emilyjia2000]

Hi all,

I met a problem when I tried to find out that the similar/different peaks between two different samples. I used MACS to detect peaks, which generate long peaks (several kb). When compared the peaks from two different samples, I chose intersectBED to deal with BED files generated from MACS. I am not sure if intersectBED is the right tool to choose, besides it generated the sum of peaks from both common and unique peaks are not equal to the number of peaks detected by sample.

Does anyone have any idea on finding common/unique peaks by two samples? I do appreciate it.

Thanks