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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">Classic quick-start guide</h1></header><article><div><span><h2><a class="anchor" aria-hidden="true" id="reference-sequences"></a><a href="#reference-sequences" 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>Reference Sequences</h2>
<p>Before loading annotation data, format your reference sequences for JBrowse using bin/prepare-refseqs.pl.</p>
<p>For FASTA format sequence files</p>
<pre><code class="hljs">bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa
</code></pre>
<p>For sequences already stored in a Bio::DB::* database, you can use prepare-refseqs.pl with a biodb-to-json.pl config, see <a href="/docs/biodb-to-json.pl.html">here</a> for details.</p>
<pre><code class="hljs">bin/prepare-refseqs.pl --conf docs/tutorial/conf_files/volvox.json
</code></pre>
<h2><a class="anchor" aria-hidden="true" id="genomic-annotations-and-features"></a><a href="#genomic-annotations-and-features" 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>Genomic annotations and features</h2>
<p>JBrowse can import feature data from flat files, or from databases that have Bio::DB::* Perl interfaces.</p>
<h3><a class="anchor" aria-hidden="true" id="bin-flatfile-to-jsonpl"></a><a href="#bin-flatfile-to-jsonpl" 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>bin/flatfile-to-json.pl</h3>
<p>If you have flat files like GFF3 or BED, it is usually best to use <code>bin/flatfile-to-json.pl</code> to import them. <code>bin/flatfile-to-json.pl</code> accepts many different command-line settings that can be used to customize the appearance of the new track. Run <code>bin/flatfile-to-json.pl</code> --help to see a description of the available settings.</p>
<pre><code class="hljs">bin/flatfile-to-json.pl --gff path/to/my.gff3 --trackType CanvasFeatures --trackLabel mygff
</code></pre>
<h3><a class="anchor" aria-hidden="true" id="bin-biodb-to-jsonpl"></a><a href="#bin-biodb-to-jsonpl" 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>bin/biodb-to-json.pl</h3>
<p>If you have a genomic annotation database such as Chado, Bio::DB::SeqFeature::Store, or Bio::DB::GFF, then you can use JBrowse's <code>biodb-to-json.pl</code>. You use <code>bin/biodb-to-json.pl</code> with a configuration file (the format of which is documented here).</p>
<pre><code class="hljs">bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json
</code></pre>
<h3><a class="anchor" aria-hidden="true" id="next-gen-reads-bam"></a><a href="#next-gen-reads-bam" 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>Next-gen reads (BAM)</h3>
<p>JBrowse can display alignments directly from BAM files, with no pre-processing necessary. To use, download the BAM file and BAM index into your data folder and you can manually edit text snippets into tracks.conf</p>
<pre><code class="hljs">[tracks.alignments]
storeClass = JBrowse/Store/SeqFeature/BAM
urlTemplate = myfile.bam
category = NGS
type = JBrowse/View/Track/Alignments2
key = BAM alignments from SEQ1654
</code></pre>
<p>Then, you will have a data structure that looks like</p>
<pre><code class="hljs">data/myfile.bam
data/myfile.bam.bai
data/tracks.conf
</code></pre>
<p>Where tracks.conf contains this above config, and then myfile.bam will be located relative to the location of tracks.conf so since they are in the same directory, it does not need any additional path qualifications. Note that urlTemplate can be a full URL path</p>
<p>Also note: BAM files are required to be sorted and indexed (i.e. have a corresponding .bai file or .csi file. If it is .csi, then the csiUrlTemplate can be used. If it is .bai, then it will automatically be located as <yourbamfile.bam> with .bai added on the end).</p>
<h4><a class="anchor" aria-hidden="true" id="next-gen-read-track-types"></a><a href="#next-gen-read-track-types" 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>Next-gen read track types</h4>
<p>JBrowse has two main track types that are designed especially for use with BAM data:</p>
<h5><a class="anchor" aria-hidden="true" id="alignments2"></a><a href="#alignments2" 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>Alignments2</h5>
<p>Shows individual alignments from the BAM file, as well as insertions, deletions, skipped regions, and SNPs encoded in the BAM's MD or CIGAR fields.</p>
<h5><a class="anchor" aria-hidden="true" id="snpcoverage"></a><a href="#snpcoverage" 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>SNPCoverage</h5>
<p>Shows a coverage histogram plot, with colored bars showing the locations of base-level mismatches and possible SNPs in the reads.
To use them, set type = Alignments2 or type = SNPCoverage in the track configuration.</p>
<h2><a class="anchor" aria-hidden="true" id="index-names"></a><a href="#index-names" 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>Index Names</h2>
<p>After loading feature data, to let users find features by typing feature names or IDs in the autocompleting search box, a special index of feature names must be generated using <code>bin/generate-names.pl</code>.</p>
<pre><code class="hljs">bin/generate-names.pl -v
</code></pre>
<p>Note: You need to re-run bin/generate-names.pl to add new feature names to the index every time you add new annotations to JBrowse using any of the *-to-json.pl scripts.</p>
<p>Also note: the track types that are indexed by bin/generate-names.pl include</p>
<ul>
<li>GFF, GBK, BED loaded via flatfile-to-json.pl. By default "ID", "Name", and "Alias" are indexed. Note that --nameAttributes can be used to index additional fields</li>
<li>Features from biodb-to-json.pl</li>
<li>VCF tabix files and GFF3 tabix files (their "ID" and "Name" field from GFF are indexed and only ID from VCF are indexed)</li>
</ul>
<p>BAM reads and BigWigs are not indexed by generate-names.pl</p>
<h2><a class="anchor" aria-hidden="true" id="quantitative-tracks-bigwig-and-wiggle"></a><a href="#quantitative-tracks-bigwig-and-wiggle" 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>Quantitative tracks (BigWig and Wiggle)</h2>
<p>JBrowse can display alignments directly from BigWig files, with no pre-processing necessary. Simply add a stanza with the relative URL of the file to your data/tracks.conf file, of the form:</p>
<pre><code class="hljs">[ tracks.my-bigwig-track ]
storeClass = JBrowse/Store/SeqFeature/BigWig
urlTemplate = myfile.bw
type = JBrowse/View/Track/Wiggle/XYPlot
key = Coverage plot of NGS alignments from XYZ
</code></pre>
<p>JBrowse has two track types that are designed especially for use with quantitative data:</p>
<h3><a class="anchor" aria-hidden="true" id="jbrowse-view-track-wiggle-xyplot"></a><a href="#jbrowse-view-track-wiggle-xyplot" 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>JBrowse/View/Track/Wiggle/XYPlot</h3>
<p>Shows quantitative data as a bar graph. See the JBrowse wiki for configuration options.</p>
<h3><a class="anchor" aria-hidden="true" id="jbrowse-view-track-wiggle-density"></a><a href="#jbrowse-view-track-wiggle-density" 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>JBrowse/View/Track/Wiggle/Density</h3>
<p>Shows quantitative data as a "heatmap" plot, which by default draws regions with positive scores as progressively more intense blue, and negative scores as progressively more intense red. See the JBrowse wiki for configuration options, including how to change the color-change point (bicolor_pivot), and the colors.</p>
<p>To use them, set type = JBrowse/View/Track/Wiggle/XYPlot or type = JBrowse/View/Track/Wiggle/Density in the track configuration.</p>
<h2><a class="anchor" aria-hidden="true" id="troubleshooting"></a><a href="#troubleshooting" 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>Troubleshooting</h2>
<p>Sometimes things just don't go well. It seems like nothing is ever as easy as it should be. Here are several resources you can use if it turns out that this guide is not enough to get JBrowse working for you.</p>
<ul>
<li><a href="faq.html#troubleshooting">JBrowse FAQ</a> - The FAQ contains extended documentation on many aspects JBrowse, including troubleshooting tips.</li>
<li>Mailing list <a href="mailto:gmod-ajax@lists.sourceforge.net">gmod-ajax@lists.sourceforge.net</a> - send an email to this mailing address and/or subscribe. If it is related to just getting started with jbrowse, please attach the setup.log file that is generated by <a href="http://setup.sh">setup.sh</a></li>
<li>GitHub at GMOD/jbrowse - This is preferably for actual JBrowse issues and feature requests but some help issues can be addressed here too :)</li>
<li>Gitter channel at <a href="https://gitter.im/GMOD/jbrowse">https://gitter.im/GMOD/jbrowse</a></li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="conclusion"></a><a href="#conclusion" 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>Conclusion</h2>
<p>Good luck and enjoy JBrowse!</p>
</span></div></article></div><div class="docs-prevnext"><a class="docs-prev button" href="/docs/tutorial.html">← Indexed file formats tutorial</a><a class="docs-next button" href="/docs/reference_sequence.html">Reference sequence configuration →</a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#reference-sequences">Reference Sequences</a></li><li><a href="#genomic-annotations-and-features">Genomic annotations and features</a><ul class="toc-headings"><li><a href="#bin-flatfile-to-jsonpl">bin/flatfile-to-json.pl</a></li><li><a href="#bin-biodb-to-jsonpl">bin/biodb-to-json.pl</a></li><li><a href="#next-gen-reads-bam">Next-gen reads (BAM)</a></li></ul></li><li><a href="#index-names">Index Names</a></li><li><a href="#quantitative-tracks-bigwig-and-wiggle">Quantitative tracks (BigWig and Wiggle)</a><ul class="toc-headings"><li><a href="#jbrowse-view-track-wiggle-xyplot">JBrowse/View/Track/Wiggle/XYPlot</a></li><li><a href="#jbrowse-view-track-wiggle-density">JBrowse/View/Track/Wiggle/Density</a></li></ul></li><li><a href="#troubleshooting">Troubleshooting</a></li><li><a href="#conclusion">Conclusion</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><h5>Docs</h5><a href="/blog">Blog</a><a href="/docs/tutorial.html">Getting Started</a></div><div><h5>Community</h5><a href="https://gitter.im/GMOD/jbrowse">Project Chat</a><a href="https://twitter.com/JBrowseGossip" target="_blank" rel="noreferrer noopener">Twitter</a></div><div><h5>More</h5><a href="https://github.com/GMOD/jbrowse">GitHub</a><a class="github-button" href="https://github.com/GMOD/jbrowse" data-icon="octicon-star" data-count-href="/GMOD/jbrowse/stargazers" data-show-count="true" data-count-aria-label="# stargazers on GitHub" aria-label="Star this project on GitHub">Star</a></div></section><section class="copyright">Copyright © 2019 Evolutionary Software Foundation</section></footer></div></body></html>