Is it possible to run DESeq with only two replicates in one group?
1 answer
This is perfectly fine. h.mon is right that more replicates are desirable and beneficial to make results more robust but n=2 and n=3 are common replicate numbers and the standard tools including DESeq2 are well-able to derive proper statistics from low replicate numbers.
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You can run DESeq2, edgeR, limma::voom, and others. The problem is your experiment you be under-powered - a minimum number of replicates to get good statistical power is 5-6 samples.