JBrowse can display GFF3, BAM, BigWig, and VCF+Tabix files directly from your local machine without the need to transfer any data to the server. To highlight a region, you can either right-click on a feature and select 'highlight this', or you can set the highlight explicitly to a certain genomic region by clicking "View -> Set highlight" in the menu bar.īeginning in JBrowse 1.10.0 you can also highlight a region with the mouse by clicking the highlighter tool (next to the Go button) and clicking and dragging to highlight a region. JBrowse Features Highlighting interesting things Uncomment it, refresh your browser, and you should now see the faceted track selector activated. The jbrowse_conf.json file in the jbrowse directory already conveniently contains this stanza, commented out. In this case, we have specified all of our track configurations in nf.
Next, we'll use to get feature data out of the database and turn it into JSON data that the web browser can use. Run this from within the jbrowse directory (you could run it elsewhere, but you'd have to explicitly specify the location of the data directory on the command line).Ĭd /var/Refresh it in your web browser, you should new see the JBrowse UI and a sequence track, which will show you the DNA base pairs if you zoom in far enough. Running bin/ also sets up the "DNA" track. The first script to run is bin/ that script is the way you tell JBrowse about what your reference sequences are.
"db_adaptor": "Bio::DB::SeqFeature::Store", "description": "GMOD Summer School 2013 P.
There are adaptors available for use with many other databases, such as Chado and Bio::DB::GFF. Here, we'll use the Bio::DB::SeqFeature::Store adaptor in "memory" mode to read a directory of files. There are four basic steps to setting up an instance of JBrowse: You should see a "Congratulations" page. run setup.sh to configure this copy of JBrowse.Wget unzip GMOD_Summer_School_2013_JBrowse.zip cd GMOD_Summer_School_2013_JBrowse/ unzip JBrowse-1.9.8.zip mv JBrowse-1.9.8 jbrowse download the demo bundle from and unzip it.JBrowse presentation Setting up JBrowse Getting JBrowseĬd /var/www sudo mkdir jbrowse_demo sudo chown ubuntu.ubuntu jbrowse_demo cd jbrowse_demo How and why JBrowse is different from most other web-based genome browsers, including GBrowse. It's also very useful to know how to tab-complete in the shell. Make sure you can copy/paste from the wiki. Sudo apt-get install libpng12-0 libpng12-dev build-essential libncurses5-dev
This is how they were installed: (don't do this yourself) Other prerequisites are installed by JBrowse automatically. samtools, and its dependency libncurses5-dev.Optional, for BAM files ( setup.sh tries to install these for you in the JBrowse directory): Optional, for generating images from Wiggle files: These have already been set up on the VM image. 4.3 Combination tracks (coming in 1.10.0).
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