<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>

CC BY-SA 3.0
2017-06-07T08:31:35.480Z
2017-06-07T08:31:35.480Z
Lucas van Dijk
<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>

<rna-seq>
How can HISAT2/StringTie report decimal coverage values
# 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

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## 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


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