For each sample (and replicate), do I have to convert zero read counts to ones (pseudo counts) while running deseq2?
I assume I don’t have to, but a quick clarification.
How exactly does DESeq2 handles with the zero counts? I tried to understand and look for it but is still unclear for me. Thanks
Here is the DESeq2 paper with details on the methods:
Counts of zero are not treated differently by the statistical model than a count of 1, 2, ...
Thank you very much.