Question: Diffbind for ATAC-seq data with no controls
0
gravatar for daniele.avancini
13 months ago by
daniele.avancini20 wrote:

Hi all, I'm trying to use Diffbind to identify differentially open regions (identified using ATAC-seq) between three different cell types. I have three biological replicates for each cell type. I'm building now the sample sheet to import the data into Diffbind, but I don't know what I should indicate as a control since ATAC do not have controls. Is there a way to avoid this problem?

atac-seq diffbind • 1.2k views
ADD COMMENTlink modified 13 months ago by Rory Stark510 • written 13 months ago by daniele.avancini20
5
gravatar for Rory Stark
13 months ago by
Rory Stark510
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark510 wrote:

Control reads, such as those from an Input sample, are optional in DiffBind, so you can just leave out the control column in the sample sheet.

ADD COMMENTlink written 13 months ago by Rory Stark510
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