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Duplicate peaks in MACS2 narrowPeak output



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  • Duplicate peaks in MACS2 narrowPeak output

    Hi Everyone,

    Has anyone noticed that MACS2 occasionally outputs duplicate peaks in the .narrowPeak output? There peaks have the exact same start and end coordinates but different scores and p-values. For example:

    chr start end H3K27me3_rep1_peak_7a 273 . 6.39200 31.40267 27.34079 201
    chr start end H3K27me3_rep1_peak_7b 26 . 2.87399 4.79406 2.64603 624

    Is there any documentation or clues about why this happens? Is it safe to merge these peaks and what can one do with the quality values?

    Any help and guidance appreciated.

    With thanks,


  • #2
    Not an answer but I am curious about the same thing.


    • #3
      Those entries refer to two summits within the same peak. Safe to merge, if you don't care about the shape of the peak.


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