Using DiffBind for ATACseq data with Multiple Conditions
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4 months ago

Hi everyone,

I'm completely new to bioinformatics, so I apologize in advance for asking a very basic question.

I have recently performed ATAC-seq using mouse heart tissues at several timepoints postnatally (5 timepoints [set as different conditions in the samplesheet], with 3 replicates each).

I have mapped the data and generated narrowpeak files for my data. Now, I wanted to conduct differential peak analysis using DiffBind, to identify peaks that are unique to each timepoint, as well as peaks that are common to all groups). I'm wondering if this is possible to do with DiffBind?

If possible, I am assuming I'd follow the steps in the vignette, but I'd have to do something different for the"dba.contrast" step, since I am not sure if "dba.contrast (DBA, categories = DBA_CONDITION)" would work, but I'm not too sure how to proceed.

Any help would be really appreciated, thanks!! :)

diffbind ATAC-seq • 229 views
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