Merge replicates for CHIP-seq analysis

Question

[michelafrancesconi9]

I am performing for the first time CHIP-seq analysis with two replicas, I used MACS2 to find the peaks of the two respective replicas, I used IDR to find the percentage of peaks in common and bedtools intersect to get a bed file that I can then convert to bedGrapgh and finally BigWig to display the peaks in common. I want to know if you also suggest me to use bedtools fisher and I was wondering if you think I should also merge the two replicas and use MACS2 on this new bam file, since the two replicas have different reads and if you can advise me how to do this and what analysis is best.

Thank you