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?
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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.
answered Jan 26 '18 at 22:00
