Are their any peak callers other than macs that can be used for paired end data ?
If yes, please describe your experience with them.
I just learnt of Genrich this week - we installed it (which went smoothly), ran it and got results that didn't seem off. So, generally, I would recommend it although you may not want to use it for the super-high impact paper that you are submitting next week because it does not seem to be published yet and reviewers may complain about that.
Is there a specific functionality you're after?
I should add that the reason we tried it out was that we found these arguments to be convincing and hitting all the complaints we've had about MACS for PE data, especially in the ATAC-seq context.
Thank's for the Genrich. I am not after any specific functionality, in general I have found that MACS2 doesn't work quite well with H3K9me3 or H3K27me3 marks (might be more). I don't know what the issue is and how it can be fixed. On the other hand PeakRanger (CCAT) works quite well with these marks.