Question: Diffbind for ATAC-seq data with no controls
gravatar for daniele.avancini
8 months ago by
daniele.avancini10 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 • 711 views
ADD COMMENTlink modified 8 months ago by Rory Stark480 • written 8 months ago by daniele.avancini10
gravatar for Rory Stark
8 months ago by
Rory Stark480
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark480 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 8 months ago by Rory Stark480
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