After viewing a narrowPeak file in IGV I found that some regions had overlapping records, each of which has a different name and different associated peak statistics. For example:
chr17 35164351 35165393 p300_EpiLC_minusActivin_peak_17078a 49 . 3.62557 7.39305 4.98814 174 chr17 35164351 35165393 p300_EpiLC_minusActivin_peak_17078b 122 . 5.43658 15.04741 12.24058 420 chr17 35164351 35165393 p300_EpiLC_minusActivin_peak_17078c 247 . 6.42027 27.98737 24.78897 823
Is this normal behaviour for MACS2? I would have thought it wrong to report three separate records for the same peak region? I called the peaks using the following command:
macs2 callpeak -t p300_EpiLC_minusActivin.filtered.bam -c p300_EpiLC_minusActivin.filtered.bam -n p300_EpiLC_minusActivin -f BAM -g mm -s 36 -q 0.01 -B --call-summits 2> p300_EpiLC_minusActivin.log
# My apologies, I have found my answer. See this excerpt from the MACS2 manual:
--call-summits
MACS will now reanalyze the shape of signal profile (p or q-score depending on cutoff setting) to deconvolve subpeaks within each peak called from general procedure. It's highly recommended to detect adjacent binding events. While used, the output subpeaks of a big peak region will have the same peak boundaries, and different scores and peak summit positions.