Question: Diffbind for ATAC-seq data with no controls
2
gravatar for daniele.avancini
2.5 years ago by
daniele.avancini60 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 • 2.7k views
ADD COMMENTlink modified 2.5 years ago by Rory Stark880 • written 2.5 years ago by daniele.avancini60
10
gravatar for Rory Stark
2.5 years ago by
Rory Stark880
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark880 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 2.5 years ago by Rory Stark880
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