Although MACS2.0 help page says the default q-value cutoff is 0.05 the .xls output file has -log(q-values) below 1.301.. = -log(0.05). I could apply the cutoff to select values above 1.3 but to use annotatePeaks.pl (for annotation) a BED file is needed. I don't see any field with q-value/-log(q-value) in BED file. How do we know which peaks in the bed file output by MACS2 are significant (with q-value < 0.05)?
Question: Which peaks in the bed file output by MACS2 are significant ?
2.6 years ago by
salamandra • 270
salamandra • 270 wrote:
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