Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-26T22:00:05.173Z
Answers.LastActivityDate: 2018-01-26T22:00:05.173Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Tags: <rna-seq><deseq2>
Title: What are the count units in DEseq2?
ThreadText: # 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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