I am trying to use DESeq2 for differential analysis of ATAC-seq data. I have performed peak calling, obtained a consensus peak data set and, using featureCounts, generated a count matrix with my samples as columns and the peak coordinates as rows. I have two conditions, 4 biological and 2 technical replicates each; so 16 samples in total. I am interested in the differences between my two conditions, so I was using DESeq2::DESeqDataSetFromMatrix with
design = ~condition
Now I am wondering about two things: 1. Should I collapse my technical replicates before running the DE pipeline? 2. Should I also include my biological replicates in the design formula? And also an interaction term (condition:BioRep)?
I am very new to this, so apologies if this is a very basic question. Appreciate input and help!