Hello I am starting to work with Faire-seq data, I am using MACS to analize it. For the moment I only have have 2 replicates of the control experiment data, sequenced and aligned to the reference genome. The problem is that when I run MACS with one of the control replicates I do not find the peaks of some regions that I already know should be there...it is an excersice to "validate" my controls. Given this, is it valid to do a "merge" of both control data alignments and feed MACS with it, in order to get improved signal?
Thank you for your help