I need your help to choose proper software for doing differential gene expression analysis of these data. they are transcript quantification from Salmon, then import them to tximport to got gene and transcript counts from RNA-seqs. actually, I have different groups and I want to do DGE for each one. I would describe conditions and samples.
in the first group, I have 8 samples named: D1 , D3, R1, and R3. each one of them has two technical replicates. for example D 1 ( D1_L001 and D1_L002); D3 (D3_L001 and D3_L002), R1(R1_L001 and R1_L002) and R3 (R3_L001 and R3_L002). on the other hand, D1 and D3 are biological replicates as well as R1 and R3. I'd like to make a comparison between total of them I mean all D vs R, and D1 vs R1, and D3 vs R3. what is your suggestion for these samples of first group to do DGE?
I did DGE by DESeq2, but its developer would not recommend DESeq2 for such conditions that compare individually and combining samples. please help me to choose best statistical software to do differential gene expression analysis for such conditions?
thanks in advance