Question: File type for DEseq using ATACseq data
0
gravatar for mw848
5 weeks ago by
mw8480
mw8480 wrote:

What are the file types that should be in my work environment in Rstudio to run DEseq on ATACseq data. I'm looking to find differential accessible regions in two samples (deleted gene vs wt)

deseq2 • 77 views
ADD COMMENTlink modified 5 weeks ago by Michael Love24k • written 5 weeks ago by mw8480

We use a counts matrix by peak number.

Do you only have 1 sample in each group?

ADD REPLYlink written 5 weeks ago by DonnyB0

Yes, I only have 1 sample per group. I have made a count matrix file using deepTools. Would that be similar? If not, how do I make a countmatrix file using either my called peak file or reads file?

ADD REPLYlink written 4 weeks ago by mw8480
Answer: File type for DEseq using ATACseq data
0
gravatar for Michael Love
5 weeks ago by
Michael Love24k
United States
Michael Love24k wrote:

This isn’t really a DESeq2 question, but more about how to analyze ATAC which is a bit out of scope of what I provide support for. I’d recommend following the steps in the methods of an ATAC-seq paper. See for example the paper that generated the data in the “macrophage” Bioc package.

ADD COMMENTlink written 5 weeks ago by Michael Love24k
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