text: user1226: 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?
  
  user77: 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.
  
original_text: 1226: <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>
   77: <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>
  