Macs2 output shows only single basepair peak instead of a section of DNA

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4.2 years ago

fdewards ▴ 10

I run chip-seq data and my output is then run through the Macs2 callpeaks program as I am trying to determine if there is a consensus sequence between different chip-data. Problem is that it shows only a single basepair peak in the UCSC display when it should be a sequence of bases. Helllp!

ChIP-Seq macs2 callpeak macs • 1.1k views

ADD COMMENT • link updated 4.2 years ago by kinalimeric ▴ 40 • written 4.2 years ago by fdewards ▴ 10

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Maybe you are looking only peak summit.

ADD REPLY • link 4.2 years ago by Prakash ★ 2.2k

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I wish that was the case but I'm not. Weird

ADD REPLY • link 4.2 years ago by fdewards ▴ 10

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Could you give the version of MACS2 you are using and specify which output file you are referring to. There should be a narrowPeak.bed file present among the results. If you also provide the command you used to perform the analysis it will help us troubleshoot it for you.

ADD REPLY • link 4.2 years ago by mark.ziemann ★ 1.9k

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