Hi all,
I cannot find good documentation on MACS2 and I do not understand how it treats paired-end data. I can see that I can use -f BAMPE to indicate that the reads are paired but I am not convinced that it is really using that information. I have removed all duplicates by pair but MACS2 is reporting that I still have 38% duplication which is what you would find if you only looked at one end of the pair, not both. Is anyone else having this same experience? I have tried both sorted and unsorted bam files in which the mates appear together.
Thanks!
Lynn
I cannot find good documentation on MACS2 and I do not understand how it treats paired-end data. I can see that I can use -f BAMPE to indicate that the reads are paired but I am not convinced that it is really using that information. I have removed all duplicates by pair but MACS2 is reporting that I still have 38% duplication which is what you would find if you only looked at one end of the pair, not both. Is anyone else having this same experience? I have tried both sorted and unsorted bam files in which the mates appear together.
Thanks!
Lynn
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