Question

Can I input peak files from Genrich as input reads in DiffBind?

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gsenevirathne • 0

@gsenevirathne-20261

Last seen 5.7 years ago

Hi,

I have been running Genrich (similar to MACS2) as way of calling peaks for my ATAC-seq analysis. My output files from the Genrich are .log and .narroPeak files. Can I use the peak files in DiffBind?

Thanks!

Gayani

DiffBind Genrich • 2.4k views

ADD COMMENT • link updated 5.7 years ago by Rory Stark ★ 5.2k • written 5.7 years ago by gsenevirathne • 0

score 2 · Answer 1 · 2019-03-25

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Rory Stark ★ 5.2k

@rory-stark-5741

Last seen 5 weeks ago

Cambridge, UK

Yes, this should work with the .narrowPeak files. In the sample sheet, the values in the PeakCaller column should be set to "narrow".

ADD COMMENT • link 5.7 years ago Rory Stark ★ 5.2k

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Thank you for the quick response! It worked.

ADD REPLY • link 5.7 years ago gsenevirathne • 0

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In genrich you can input all the replicates for a group and get one .narrowPeak file. Is it ok for the DiffBind sampleSheet to have the same .narrowPeak file for multiple replicates? Or do we need to generate a unique peak file for each sample/replicate?