question

[mannekim]

Hi, this is not really an issue but more of a question.
For the normalized counts ouput, is it in RPKM?

[igordot]

The normalized counts (counts.normalized.csv or counts.normalized.xlsx) are scaled by size factors. This is the standard DESeq2 normalization. FPKMs are available as well (counts.fpkm.csv or counts.fpkm.xlsx).