JBrowse

Tips and tricks

How can I get jbrowse to update the URL of a parent page when jbrowse is inside of an iframe

You can use code such as this

<iframe id="jbrowse_iframe" src="/jbrowse/" scrolling="no" style="width:100%;height:800px;"></iframe>

<script>

//https://stackoverflow.com/questions/2090551/parse-query-string-in-javascript
function getQueryVariable(variable) {
    var query = window.location.search.substring(1);
    var vars = query.split('&');
    for (var i = 0; i < vars.length; i++) {
        var pair = vars[i].split('=');
        if (decodeURIComponent(pair[0]) == variable) {
            return decodeURIComponent(pair[1]);
        }
    }
}
// subscribe to jbrowse movements inside of the iframe and update parent page url
var datadir = getQueryVariable('data');
var iframe = document.getElementById('jbrowse_iframe');
iframe.addEventListener('load', function() {
    var JBrowse = iframe.contentWindow.JBrowse;
    JBrowse.subscribe( '/jbrowse/v1/n/navigate',  function(obj) {
        var shareURL = JBrowse.makeCurrentViewURL();
        var parser = new URL(shareURL);
        window.history.replaceState( {}, "", parser.search );
    });
});
// pass the parameters from the parent page into the iframe
iframe.src = iframe.src + window.location.search;

</script>

With this setup, you can pass URL parameters from the URL of the parent page e.g. http://localhost/parent_page/?data=mydata&loc=chr1:1..10000 and it will forward those URL params to the jbrowse instance (located at http://localhost/jbrowse) and the URL will be autoupdated when you change locations

Can I use JBrowse with phantomJS?

Yes! See http://gmod.org/wiki/JBrowse_Configuration_Guide#Rendering_high_resolution_screenshots_using_PhantomJS for an example

Puppeteer also works

Can I run JBrowse on GitHub pages?

Yes! Upload jbrowse to a gh-pages branch on a github repo, and also put a .nojekyll file in the root directory.

This bypasses the normal jekyll parser of github and allows jbrowse to load https://github.com/blog/572-bypassing-jekyll-on-github-pages

What is the benefit of using biodb-to-json.pl?

  • You can store more advanced creation in the biodb-to-json.pl conf file, allowing for more advanced and reproducible builds of your data directory
  • You can load data from different sources like Chado, GFF, etc.

In general, using normal commands like flatfile-to-json, prepare-refseqs, etc work fine though. See setup.sh for how the volvox sample data combines using biodb-to-json and other techniques.

Can I make an ultra-compact setting on my features?

Yes you can!

The styles on "CanvasFeatures" include normal, compact, and collapse

By default, compact divides the height of glyphs by 4, so if you make the height of your features smaller with style->height then when you set compact it will be ultra compact.

Can I disable the histograms on a track?

Yes! Try setting style.featureScale to a very small number like 0.0000000001 (but greater than 0)

Can I visualize junctions from RNA-seq data

Yes, try out the SashimiPlot plugin! https://github.com/cmdcolin/sashimiplot

It dynamically calculates the splicing coverage of a track or uses junctions.bed files for junctions

Can I view GCContent on my sequence data?

Yes, the GCContent plugin will calculate the GCContent from your sequence data automatically. See https://github.com/cmdcolin/gccontent

It works fairly well on mid-size genomes. If you have very large megabase scale assemblies, then you might consider pre-calculating the GCContent.

Can I view GWAS results in JBrowse?

Yes, the GWASViewer plugin does this. https://github.com/cmdcolin/gwasviewer/

What do the colors mean on the BAM files for JBrowse

  • Light red is a forward read that is paired
  • Super light red is a forward read that is badly paired
  • Dark red is a forward read that is missing a pair
  • Light blue is a reverse read that is paired
  • Super light blue is a reverse read that is badly paired
  • Dark blue is a reverse read that is missing a pair
  • Grey/black is a read whose pair is on another chromosome

Can I use RNA-seq with JBrowse

Yep! The regular alignments track types (e.g. JBrowse/View/Track/Alignments2) supports RNA-seq and will show spliced alignments.

Also, there are two special options for RNA-seq that can help decipher the reads.

  • The "Use XS" option is a RNA-seq specific flag that aligners output which detects the strand that a read came from according to canonical splice site. Enable in config using useXS: true
  • The "Use reversed template" option is flag normally used for "stranded paired-end RNA-seq" data and it will make both reads in a pair look like they are in the same direction, so for example, reads from a plus-strand gene will all appear red, even when one of the reads in the pair would normally be blue. Enable in config with useReverseTemplate: true

Can I use long reads with JBrowse?

Long reads from platforms like nanopore and pacbio pose some challenges but will work if it is in BAM format. The JBrowse 1.12.3 release also includes an optimization, cacheMismatches, to enhance speed on long read tracks. This must be enabled manually in the config at the moment.

Can I have subtracks in JBrowse?

You can make a custom plugin to do this. The "multibigwig" plugin is an example of this https://github.com/cmdcolin/multibigwig

How do I get coverage for a BAM file?

  1. Use the SNPCoverage track
  2. Use the FeatureCoverage track type
  3. Make a bigwig for your BAM file (recommend: use "bedtools genomecov" to convert the BAM to bedgraph, and the convert bedgraph to bigwig with UCSC bedGraphToBigWig)

Also note: with the third option, you can make it so that your BAM track has a bigwig when zoomed out, but then shows the reads when zoomed in. Any CanvasFeatures track can use a bigwig for summary histograms. The Alignments2 volvox-sorted.bam track is an example of this. See http://gmod.org/wiki/JBrowse_Configuration_Guide#Configuring_Summary_Histograms

Can I zoom even closer to the base level?

Yes. You can set the config variable view.maxPxPerBp to a higher value. To increase, try setting this in jbrowse.conf

view.maxPxPerBp=50

Note sometimes the "translations" will appear wrong at high zoom levels, so don't depend on this for the protein translations

By default, the max zoom level is 25, so setting it to 50 makes you able to zoom in twice as much.

How do I change the color of bigwig dynamically

The pos_color and neg_color config variables for BigWig tracks accept callback functions. The phytozome browser has good examples of this with the VISTA plot tool

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