@gmod/jbrowse
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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">Data export</h1></header><article><div><span><p>Starting with version 1.7.0, JBrowse users can export track data in a variety of formats for either specific regions, or for entire reference sequences. Export functionality can also be limited and disabled on a per-track basis using the configuration variables listed below.</p>
<h2><a class="anchor" aria-hidden="true" id="data-formats"></a><a href="#data-formats" 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>Data Formats</h2>
<p>Current supported export data formats are:</p>
<ul>
<li>FASTA (sequence tracks)</li>
<li>GFF3 (all tracks)</li>
<li>bed (feature and alignment tracks)</li>
<li>bedGraph (wiggle tracks)</li>
<li>Wiggle (wiggle tracks)</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="export-configuration"></a><a href="#export-configuration" 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>Export Configuration</h2>
<p>Each track in JBrowse that can export data supports the following configuration variables.</p>
<table>
<thead>
<tr><th>Option</th><th>Value</th></tr>
</thead>
<tbody>
<tr><td><code>noExport</code></td><td>If true, disable all data export functionality for this track. Default false.</td></tr>
<tr><td><code>maxExportSpan</code></td><td>Maximum size of the a region, in bp, that can be exported from this track. Default 500 Kb.</td></tr>
<tr><td><code>maxExportFeatures</code></td><td>Maximum number of features that can be exported from this track. If "Save track" is unexpectedly greyed out, inspect this setting. Default: 50000</td></tr>
<tr><td><code>maxFeatureSizeForUnderlyingRefSeq</code></td><td>Maximum length of sequence to be displayed in the popup boxes. Default: 250kb</td></tr>
</tbody>
</table>
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