Question

File type for DEseq using ATACseq data

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mw848 • 0

@mw848-21345

Last seen 5.4 years ago

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 • 674 views

ADD COMMENT • link updated 5.4 years ago by Michael Love 43k • written 5.4 years ago by mw848 • 0

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We use a counts matrix by peak number.

Do you only have 1 sample in each group?

ADD REPLY • link 5.4 years ago D ▴ 10

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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 REPLY • link 5.4 years ago mw848 • 0

score 0 · Answer 1 · 2019-07-14

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Michael Love 43k

@mikelove

Last seen 17 hours ago

United States

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 COMMENT • link 5.4 years ago Michael Love 43k