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Question: Sample order in Deseq2?
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gravatar for vebaev
11 months ago by
vebaev • 130
vebaev • 130 wrote:

Hi, are the right order in Deseq2 is first "treated" and second "control" to produce changed expression in the treated sample?

Thanks!
differential de rna-seq deseq2 expression • 387 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by vebaev • 130
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gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Using Treated as the first factor is most likely what you want to do. The example under "What it does > Inputs" of the lower help section for the tool has an example that addresses your use-case.

As with most tools, options are explained on the tool form (abbreviated) and these match up with the underlying wrapped tool's linked manual help (and often publication). Many tools also have a google group/support resource and are frequently discussed by the larger Bioinformatics community at https://www.biostars.org/. Scientific advice would be applicable whether using the tool in Galaxy or not.

Hope that helps! Jen, Galaxy team
ADD COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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