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JBrowse - client-side genome browser
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class="navItem" href="/docs/flatfile-to-json.pl.html">flatfile-to-json.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/remove-track.pl.html">remove-track.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/ucsc-to-json.pl.html">ucsc-to-json.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/generate-names.pl.html">generate-names.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/prepare-refseqs.pl.html">prepare-refseqs.pl</a></li><li class="navListItem"><a class="navItem" href="/docs/biodb-to-json.pl.html">biodb-to-json.pl</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">JBrowse Desktop</h3><ul><li class="navListItem"><a class="navItem" href="/docs/jbrowse_desktop.html">JBrowse Desktop</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">FAQ</h3><ul><li class="navListItem"><a class="navItem" href="/docs/faq.html">JBrowse FAQ</a></li></ul></div><div class="navGroup"><h3 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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Minimal JBrowse configurations</h1></header><article><div><span><h1><a class="anchor" aria-hidden="true" id="minimal-configs"></a><a href="#minimal-configs" 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>Minimal configs</h1>
<p>In 1.15.3, many track types were given the ability to "auto-infer" track type and storeClass from the file extension of the urlTemplate so minimal configs can be specified</p>
<p>For example you can simply create a "data directory" folder, and hand edit a "tracks.conf" file to contain something like</p>
<pre><code class="hljs">[GENERAL]
refSeqs=genome.fa.fai
[tracks.refseqs]
urlTemplate=genome.fa
[tracks.mybam]
urlTemplate=alignments.bam
[tracks.mycram]
urlTemplate=alignments.cram
[tracks.myvcftabix]
urlTemplate=variants.vcf.gz
[tracks.mygfftabix]
urlTemplate=genes.gff3.gz
[tracks.mybedtabix]
urlTemplate=peaks.bed.gz
</code></pre>
<p>The refSeqs config tells JBrowse the list of chromosomes, which can be an FAI file, a 2bit file, a chrom.sizes file, or if prepare-refseqs.pl was used, it is unnecessary to specify this.</p>
<h3><a class="anchor" aria-hidden="true" id="sequence-track-minimal-config"></a><a href="#sequence-track-minimal-config" 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>Sequence track minimal config</h3>
<p>For the sequence track, specifying the urlTemplate as genome.fa will assume that indexed FASTA is used and will automatically locate genome.fa.fai (unindexed fasta is too slow for even modest sized reference sequences so it just assumes indexed FASTA)</p>
<pre><code class="hljs">[tracks.refseqs]
urlTemplate=genome.fa
</code></pre>
<h3><a class="anchor" aria-hidden="true" id="feature-track-minimal-config"></a><a href="#feature-track-minimal-config" 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 track minimal config</h3>
<p>To specify genes, you can use GFF3Tabix or BigBed</p>
<pre><code class="hljs">[tracks.mygfftabix]
urlTemplate=genes.gff3.gz
[tracks.mybigbed]
urlTemplate=genes.bb
</code></pre>
<p>Note GFF3Tabix supports indexing feature names, IDs, and other things (if nameAttributes is specified in the config of a GFF3Tabix, it indexes those features) with generate-names.pl. BigBed does not currently have generate-names.pl support</p>
<h3><a class="anchor" aria-hidden="true" id="alignments"></a><a href="#alignments" 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>Alignments</h3>
<p>Alignments tracks can be specified with CRAM and BAM using the minimal config</p>
<pre><code class="hljs">[tracks.mybam]
urlTemplate=alignments.bam
[tracks.mycram]
urlTemplate=alignments.cram
</code></pre>
<p>The BAM index (bai) and CRAM index (crai) will automatically be located. If CSI indexes are used, csiUrlTemplate must be specified. Or if the BAI/CRAI index is in a non-standard location, specify baiUrlTemplate/craiUrlTemplate.</p>
<h3><a class="anchor" aria-hidden="true" id="variants"></a><a href="#variants" 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>Variants</h3>
<p>A minimal VCF tabix track can use</p>
<pre><code class="hljs">[tracks.myvcf]
urlTemplate=variants.vcf.gz
</code></pre>
<p>The tbi index will automatically be located by adding .tbi to the urlTemplate. If CSI indexes are used, csiUrlTemplate must be specified</p>
<h3><a class="anchor" aria-hidden="true" id="bigwig"></a><a href="#bigwig" 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>BigWig</h3>
<p>A minimal bigwig config is simply a url template to the bigwig file</p>
<pre><code class="hljs">[tracks.mybw]
urlTemplate=bigwig.bw
</code></pre>
<h2><a class="anchor" aria-hidden="true" id="specifying-minimal-json-configs"></a><a href="#specifying-minimal-json-configs" 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>Specifying minimal JSON configs</h2>
<p>The trackList.json also can do minimal configs. An example</p>
<pre><code class="hljs">{
"refSeqs": "genome.fa.fai",
"tracks": [
{"label": "refseqs", "urlTemplate": "genome.fa"},
{"label": "bam", "urlTemplate": "alignments.bam"},
{"label": "cram", "urlTemplate": "alignments.cram"},
{"label": "vcf", "urlTemplate": "variats.vcf.gz"},
{"label": "gff3tabix", "urlTemplate": "genes.gff3.gz"},
{"label": "bigbed", "urlTemplate": "bigbed.bb"},
{"label": "bigwig", "urlTemplate": "bigwig.bw"}
]
}
</code></pre>
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