I have been using macs2 for peak calling and posterior differential peak calling. I am working with paired-end data. After calling peaks with macs2 callpeak -B option i use macs2 bdgdiff for differential analysis.
I have observed that, for some contrasts, results look better when I do not use -BAMPE option in the first call to "callpeak". Is that a normal behavior?
When running bdgdiff I have to set the -c (cutoff) at 45 to get reasonable results. Also values in the log ratio of likelihood in the output range from very high values (10³⁵) to very big negative values. Is this the cutoff a reasonable value? are this results normal?
Thank you very much,