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Old 03-24-2016, 04:05 PM   #1
deep639
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Default MACS2 broad peak calling

Is there an explanation for what the broad-cutoff means for broad peak calling for MACS. In the documentation for MACS they say it is a q-value cutoff for a broad peak region? I ask because in my result file, I still see peaks that have a -log10(qvalue) of less than the cutoff, so if my cutoff is 0.1 (the default), I see peaks that have a -log10(qvalue) of less than 1. Unless of course this is not what the broad-cutoff refers to? Thanks.
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