MACS2 and duplicates

Question

[blur]

Hi, I have an RNA seq file and I want to do peak calling through macs2. I want to know if I fist need to remove duplicates, or does macs2 remove them by default/can be told to remove them. I looked into the documentation but only saw an option to remove duplicates and create bed file all at the same time...

[harold.smith.tarheel]

Er, do you mean DNA-Seq file? MACS is a peak-calling software...

[blur]

Yes, RNAseq files I have aligned to a genome and that I want to do peak calling for.

[harold.smith.tarheel]

Without knowing why you're using RNA data for peak-calling, it's hard to advise whether duplicate removal is correct or not. Would you provide more information about your experiment/objective?