Question

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

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gsenevirathne • 0

@gsenevirathne-20261

Last seen 6.6 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 • 2.8k views

ADD COMMENT • link updated 6.6 years ago by Rory Stark ★ 5.2k • written 6.6 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 10 months 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 6.6 years ago Rory Stark ★ 5.2k

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Thank you for the quick response! It worked.

ADD REPLY • link 6.6 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?