MACS does not use any quality filters and if a read is mapped to different locations it will count it just as many times. It only removes reads that it considers to be duplicates (same start coordinate).
Reads that map to multiple locations should have mapping quality 0, so you can throw them out using samtools view -q 1
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ChIPseq question (MACS)
Hi all,
Does anyone knows if MACS uses the alignment quality score written in the SAM file, or does it use any alignment in the input SAM file?
Also - How does it cope with a read that was mapped to different locations in the genome? Does it ignore it or randomly pick one location for it, as I heard other programs do?
Thanks,
Rachelly
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