For clarities sake my experimental setup is: 2 conditions (treated + non treated), with 3 replicated per condition.
This was sequenced using paired end Hiseq.
I mapped to reference genome using TopHat2 and counted the reads using htseq-count for all of the alignments separately.
I am about to run DESeq2 on these outputs.
Clearly my Factor1 and Factor 2 are treated and non treated respectively.
My qyesiotnv is ca I use a dataset collection as an input. So can I input the replicates as three input files, or do I have to somehow merge the replicated form the treatment and then the replicates from non-treated before inputting into DESeq2?