Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-07T08:31:35.480Z
Answers.LastActivityDate: 2017-06-07T08:31:35.480Z
Answers.UserDisplayName: Lucas van Dijk
Body: <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>
  
Tags: <rna-seq>
Title: How can HISAT2/StringTie report decimal coverage values
ThreadText: # How can HISAT2/StringTie report decimal coverage values
  
  (Asked by: username_0 on 2017-06-07)
  
  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](http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html).
  
  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?
  
  **Tags:** rna-seq
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-06-07. Score: 6 | Accepted answer
  
  I suspect this is average coverage across the transcript or exon.
  
  Formula for average coverage:
  
  ![coverage-formula](https://latex.codecogs.com/gif.latex?Cov%20%3D%20N%20%5Ccdot%20%5Cfrac%7BL%7D%7BT%7D)
  
  Where:
  
  * N: number of reads mapping/aligning to your transcript/exon
  * L: average read length
  * T: Transcript/exon length
  
  
  ---
  
  