Multiple conditions comparsion

[LOYON2019]

Hello, I have 6 samples with 3 replicates. like A, B....F.
However, I am not sure how to do multiple analysis in one run, I need compare A:B, C:D, E:F, A:C, A:E, B:D, B:F. Could anyone has a suggestion? thank you.

[hartleys]

Define sample and define replicate. Are the replicates biological replicates or technical? ie did you take the same biological sample and run it on three sequencing runs, or did you take 3 biological samples from the same condition (or maybe from the same tumor sample) and do library prep and sequencing runs on that?