CHIP-SEQ - multiply aligned reads handling

Question

[kozaleo]

Do I need to filter out reads that have been aligned more than once before peakcalling with MACS2?

[Bastien Hervé]

https://groups.google.com/forum/#!topic/macs-announcement/ASQ3GsXQC1c

Depends on the data you are trying to process. If your regions of interest are not repeated you can filter out them before peakcalling