Why does MACS2 report multiple records for the same peak region?
0
7
Entering edit mode
6.6 years ago
James Ashmore ★ 3.2k

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.

 

ChIP-Seq macs2 macs • 4.8k views
ADD COMMENT
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 1435 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6