I am analyzing an RNAseq with 6 conditions using deseq2. I have 6 biological replicates for control, however for the other 5 conditions (say C1,C2,C3,C4,C5) I have no replicates. Ideally, I would like to do a variance estimation using the 6 replicates for the control, and using it compare any two condition C1 vs C2. Does the standard workflow takes care of this?
thanks in advances