<p>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.</p>

CC BY-SA 3.0
2018-01-26T22:00:05.173Z
2018-01-26T22:00:05.173Z
Devon Ryan
<p>This is a pretty silly/simple question, I suppose.</p>

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

<rna-seq><deseq2>
What are the count units in DEseq2?
# What are the count units in DEseq2?

(Asked by: username_0 on 2018-01-26)

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?

**Tags:** rna-seq, deseq2

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## 1 answers

### Answer by username_1 on 2018-01-26. Score: 7 | Accepted answer

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.


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