Using DESeq2 for RNAseq analysis for two samples and a control with two replicates each

Question

[MAPK]

Hi Everyone, I have 2 different samples and one Control (Sample_A, Sample_B and Control) and two replicates for each. So the data matrix I have contains six different columns for fold counts for Sample_A1, Sample_A2, Sample_B1, Sample_B2, Control_1, Control_2. I want to know how I can use DESeq2 tool for this data matrix and do my RNAseq analysis. Can someone please clarify. Thanks.

rna-seq

Answer 1

[Asaf]

You can have a look at the beginners PDF tutorial. In the results function you can test each condition against the background using the contrast parameter.