Question: Why does MACS2 report multiple records for the same peak region?
gravatar for James Ashmore
5.4 years ago by
James Ashmore3.1k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore3.1k wrote:

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:


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.


chip-seq macs2 macs • 3.9k views
ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by James Ashmore3.1k

For cross-reference: C: Why are there duplicate peaks in ENCODE ATAC-seq output?

ADD REPLYlink written 5 months ago by ATpoint46k
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