What are the count units in DEseq2?

Question

This is a pretty silly/simple question, I suppose.

What units are DESeq2 counts? Or are the units arbitrary but internally consistent estimate of actual reads?

Answer 1

The counts are "reads" for single-end datasets and "fragments" for paired-end datasets. In other words, they're what featureCounts and htseq-count produce. The "normalized counts" that you'll be able to access in DESeq2 are, as aptly named, simply normalized versions such that values are comparable across samples.