text: user186: I have performed RNA-seq analysis using HISAT2 & StringTie workflow suggested in: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. 
  Some of the transcripts/exons have decimal coverage values (eg., 1.1 or 2.59).  
  My question is: How can these tools report decimal coverage? If only half of the read overlaps exon will this exon have 0.5 coverage?
  
  user81: I suspect this is average coverage across the transcript or exon. 
  Formula for average coverage:
  
  Where:
  
  N: number of reads mapping/aligning to your transcript/exon
  L: average read length
  T: Transcript/exon length
  
  
original_text: 186: <p>I have performed RNA-seq analysis using HISAT2 &amp; StringTie workflow suggested in: <a href="http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html" rel="noreferrer">Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown</a>. </p>
  
  <p>Some of the transcripts/exons have decimal coverage values (eg., 1.1 or 2.59).  </p>
  
  <p><strong>My question is:</strong> How can these tools report decimal coverage? If only half of the read overlaps exon will this exon have 0.5 coverage?</p>
   81: <p>I suspect this is average coverage across the transcript or exon. </p>
  
  <p>Formula for average coverage:</p>
  
  <p><img src="https://latex.codecogs.com/gif.latex?Cov%20%3D%20N%20%5Ccdot%20%5Cfrac%7BL%7D%7BT%7D" alt="coverage-formula"></p>
  
  <p>Where:</p>
  
  <ul>
  <li>N: number of reads mapping/aligning to your transcript/exon</li>
  <li>L: average read length</li>
  <li>T: Transcript/exon length</li>
  </ul>
  