DESeq2 in usegalaxy

My main factor is treatment (before and after treatment). I would like to know the gene differentially expressed because of the treatment, and to know the gene differentially expressed because of the drug(single drug vs double drug).

So, I run DESeq2 in usegalaxy with only one factor (treatment) with the following 3 levels:

treated-single drug treated-double drug untreated

I have three output from DEsq2 results file: treated single drug vs untreated treated double drug vs untreated treated single drug vs treated double drug

So, my question is this design acceptable, and how to get one file for the gene expression after filtering (P-adj <0.05 and log2(FC) >1 ). Shall I make separately and join the result in one table.

Hi @wmsalsah,
the experiment design is adequate for the second part of the question. As for the first part: it depends on the outcomes. Single and double drug can have similar effect with small or big difference, or different effects. Maybe start with Venn diagram. If one and double dozes produce similar response, maybe try DESeq2 using factor with two levels.
Kind regards,