I have a RNA seq data which I am trying to identify DEGs.
Untreated - 2 replicates (time point 0hr)
Treated - 4 replicates (2 replicates at 6hr and 2 replicates at 12 hr)
I merged all the samples and tried to identify DEGs untreated vs treated.
Is it correct to merge all samples and compare. Or should I compare the two time point treated samples with untreated as 0hr vs 6hr and 0hr vs 12hr.