I analysed 3 chip-seq replicates (each with its own input control) using macs2. For two of the samples the model produced by macs2 looked fine. I am pasting an example below:
For one of the samples the model graph for both the forward and the reverse tags seems to exhibit double peaks:
This normally happens if you mix libraries of different fragment sizes but this is not the case. Shall I be concerned? What would you do?