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JBrowse - client-side genome browser
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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Feature Coverage Tracks</h1></header><article><div><span><h1><a class="anchor" aria-hidden="true" id="feature-coverage-tracks"></a><a href="#feature-coverage-tracks" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Feature Coverage Tracks</h1>
<p>Introduced in JBrowse 1.7.0, feature coverage tracks show a dynamically-computed XY-plot of the depth of coverage of features across a genome. One good use of this track type is to provide a quick coverage plot directly from a BAM file. However, since this track calculates coverage on the fly, it can be very slow when used with large regions or very deep coverage. In this case, it is recommended to generate a BigWig file containing the coverage data, and display it with a <code>Wiggle/XYPlot</code> or <code>Wiggle/Density</code> track.</p>
<p>Feature coverage tracks are a special type of Wiggle/XYPlot tracks, so the same configuration options apply. There is an additional caveat, however: this kind of track requires the <code>min_score</code> and <code>max_score</code> variables in order to set the Y-axis scaling, since these cannot be quickly determined from raw BAM or other feature data.</p>
<p>Note: The SNPCoverage track and FeatureCoverage tracks are very similar, except the SNPCoverage track (in addition to showing SNPs) also has the extra ability to filter the supplementary/secondary reads, and other reads, so they may appear to report different coverages by default.</p>
<h2><a class="anchor" aria-hidden="true" id="example-feature-coverage-track-configuration-for-a-bam-file"></a><a href="#example-feature-coverage-track-configuration-for-a-bam-file" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Example Feature Coverage Track Configuration for a BAM file</h2>
<pre><code class="hljs css languages- {.javascript}"> {
<span class="hljs-attr">"storeClass"</span> : <span class="hljs-string">"JBrowse/Store/SeqFeature/BAM"</span>,
<span class="hljs-attr">"urlTemplate"</span> : <span class="hljs-string">"../../raw/volvox/volvox-sorted.bam"</span>,
<span class="hljs-attr">"label"</span> : <span class="hljs-string">"volvox-sorted.bam_coverage"</span>,
<span class="hljs-attr">"type"</span> : <span class="hljs-string">"JBrowse/View/Track/FeatureCoverage"</span>,
<span class="hljs-attr">"min_score"</span> : <span class="hljs-number">0</span>,
<span class="hljs-attr">"max_score"</span> : <span class="hljs-number">35</span>,
<span class="hljs-attr">"key"</span> : <span class="hljs-string">"volvox-sorted Coverage"</span>
}
</code></pre>
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