I have two replicates from one cell type (chip-seq data). I aligned each one in galaxy using bwa. I then did peak calling using MACS for each one separately because I was unable to successfully merge the BAM files and then peak call them together in one BAM file.
Now I have the peak models for each replicate and want to note the number of peaks observed. How do I this? Also, how do I overlap and compare the peaks of the two replicates so I can note the overall number of peaks?