This JBrowse tutorial was presented by Scott Cain at the Plant and Animal Genomes Meeting in January 2015 using JBrowse 1.11.5.
This tutorial assumes an Ubuntu 14.04.1 VirtualBox appliance (2.3 GB) that was distributed before the course.
Prerequisites are installed by JBrowse automatically. A few things may fail to install (like legacy support for wiggle files), but that doesn’t matter.
Make sure you can copy/paste from the wiki.
It’s also very useful to know how to tab-complete in the shell.
It’s probably a good idea to use a browser like Chrome that has the ability to turn off caching while working on this tutorial. To do this in Chrome, with the browser open to the JBrowse page you’re working on, select Developer->Javascript Console from the View menu. In the console, click the “gear” icon (settings) and check the box labeled “Disable Cache”.
How and why JBrowse is different from most other web-based genome browsers, including GBrowse.
More detail: paper
cd /var/www/html
mkdir jbrowse_demo
cd jbrowse_demo
#wget https://s3.amazonaws.com/jbrowse-tutorials/PAG_2015_JBrowse.zip -- already in /var/www/html
mv ../PAG_2015_JBrowse.zip .
unzip PAG_2015_JBrowse.zip
cd PAG_2015_JBrowse
unzip JBrowse-1.11.5.zip
mv JBrowse-1.11.5 jbrowse
setup.sh to configure this copy of JBrowsecd jbrowse
./setup.sh
Visit in web browser:
http://localhost/jbrowse_demo/PAG_2015_JBrowse/jbrowse/index.html
You should see a “Congratulations” page.
There are four basic steps to setting up an instance of JBrowse:
Here, we’ll use the Bio::DB::SeqFeature::Store adaptor in “memory” mode to read a directory of files. There are adaptors available for use with many other databases, such as Chado and Bio::DB::GFF.
Config file: pythium-1.conf
{
"description": "GMOD Summer School 2013 P. ultima Example",
"db_adaptor": "Bio::DB::SeqFeature::Store",
"db_args" : {
"-adaptor" : "memory",
"-dir" : ".."
},
...
The first script to run is bin/prepare-refseqs.pl; that script is the
way you tell JBrowse about what your reference sequences are. Running
bin/prepare-refseqs.pl also sets up the “DNA” track.
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).
cd /var/www/html/jbrowse_demo/PAG_2015_JBrowse/jbrowse
bin/prepare-refseqs.pl --gff ../scf1117875582023.gff
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.
Next, we’ll use biodb-to-json.pl to get feature data out of the
database and turn it into JSON data that the
web browser can use.
In this case, we have specified all of our track configurations in
pythium-1.conf.
...
"TRACK DEFAULTS": {
"class": "feature"
},
"tracks": [
{
"track": "Genes",
"key": "Genes",
"feature": ["mRNA"],
"autocomplete": "all",
"class": "transcript",
"subfeature_classes" : {
"CDS" : "transcript-CDS",
"UTR" : "transcript-UTR"
}
},
...
]
track specifies the track identifier (a unique name for the track, for
the software to use). This should be just letters and numbers and - and
_ characters; using other characters makes things less convenient.
key specifies a human-friendly name for the track, which can use any
characters you want.
feature gives a list of feature types to include in the track.
autocomplete including this setting makes the features in the track
searchable.
urltemplate specifies a URL pattern that you can use to link genomic
features to specific web pages.
class specifies the CSS class that
describes how the feature should look.
For this particular track, I’ve specified the transcript feature
class.
Run the bin/biodb-to-json.pl script with this config file to format
this track, and the others in the file:
bin/biodb-to-json.pl --conf ../pythium-1.conf
Refresh JBrowse in your web browser. You should now see a bunch of annotation tracks.
When you generate JSON for a track, if you specify "autocomplete" then
a listing of all of the feature names from that track (along with
feature locations) will also be generated and used to provide feature
searching and autocompletion.
The bin/generate-names.pl script collects those lists of names from
all the tracks and combines them into one big tree that the client uses
to search.
bin/generate-names.pl -v
Visit in web browser, try typing a feature name, such as maker-scf1117875582023-snap-gene-0.26-mRNA-1. Notice that JBrowse tries to auto-complete what you type.
We’re going to add a couple more tracks that come from a flat file,
repeats.gff. To get feature data from flat files into JBrowse, we use
flatfile-to-json.pl.
bin/flatfile-to-json.pl --trackType CanvasFeatures \
--trackLabel repeatmasker \
--type match:repeatmasker --key RepeatMasker \
--className generic_parent \
--subfeatureClasses '{"match_part" : "feature"}' --gff ../repeats.gff
bin/flatfile-to-json.pl --trackType CanvasFeatures \
--trackLabel repeatrunner \
--type protein_match:repeatrunner \
--key RepeatRunner --className generic_parent \
--subfeatureClasses '{"match_part" : "feature"}' --gff ../repeats.gff
Visit in web browser; you should see the two new RepeatMasker and RepeatRunner tracks.
JBrowse can display alignments directly from a BAM file on your web server. Simply place the BAM file in a directory accessible to your web server, and add a snippet of configuration to JBrowse to add the track, similar to:
{
"label" : "bam_alignments",
"key" : "BAM alignments",
"storeClass" : "JBrowse/Store/SeqFeature/BAM",
"urlTemplate" : "../../simulated-sorted.bam",
"type" : "Alignments2"
}
This can be added by either editing the data/trackList.json file with
a text editor, or by running something like this at the command line to
inject the track configuration:
echo '{
"label" : "bam_alignments",
"key" : "BAM alignments",
"storeClass" : "JBrowse/Store/SeqFeature/BAM",
"urlTemplate" : "../../simulated-sorted.bam",
"type" : "Alignments2"
}' | bin/add-track-json.pl data/trackList.json
We can have JBrowse calculate the coverage of the reads in the BAM file automatically:
{
"label" : "bam_coverage",
"key" : "BAM Coverage",
"storeClass" : "JBrowse/Store/SeqFeature/BAM",
"urlTemplate" : "../../simulated-sorted.bam",
"type" : "SNPCoverage"
}
or
echo '
{
"label" : "bam_coverage",
"key" : "BAM Coverage",
"storeClass" : "JBrowse/Store/SeqFeature/BAM",
"urlTemplate" : "../../simulated-sorted.bam",
"type" : "SNPCoverage"
}
' | bin/add-track-json.pl data/trackList.json
This coverage plot also includes information about the mismatches in individual reads.
JBrowse can display quantitative data directly from a BigWig file on your web server. Simply place the BigWig file in a directory accessible to your web server, and add a snippet of configuration to JBrowse to add the track, similar to:
{
"label" : "bigwig_bam_coverage",
"key" : "BigWig - BAM coverage",
"storeClass" : "BigWig",
"urlTemplate" : "../../simulated-sorted.bam.coverage.bw",
"type" : "JBrowse/View/Track/Wiggle/XYPlot",
"variance_band" : true
}
This can be added by either editing the data/trackList.json file with
a text editor, or by running something like this at the command line to
inject the track configuration:
echo ' {
"label" : "bigwig_bam_coverage",
"key" : "BigWig - BAM coverage",
"storeClass" : "BigWig",
"urlTemplate" : "../../simulated-sorted.bam.coverage.bw",
"type" : "JBrowse/View/Track/Wiggle/XYPlot",
"variance_band" : true
} ' | bin/add-track-json.pl data/trackList.json
JBrowse can also display VCF variation data directly from a VCF file on your web server that has been compressed with Heng Li’s bgzip and tabix. Simply place the .vcf.gz and .vcf.gz.tbi files in a directory accessible to your web server, and add a snippet of configuration to JBrowse to add the track, similar to:
{
"label" : "bam_variation",
"key" : "VCF simulated variation",
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
"urlTemplate" : "../../simulated-sorted.vcf.gz",
"type" : "HTMLVariants"
}
This can be added by either editing the data/trackList.json file with
a text editor, or by running something like this at the command line to
inject the track configuration:
echo ' {
"label" : "bam_variation",
"key" : "VCF simulated variation",
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
"urlTemplate" : "../../simulated-sorted.vcf.gz",
"type" : "HTMLVariants"
} ' | bin/add-track-json.pl data/trackList.json
JBrowse has a very powerful faceted track selector that can be used to search for tracks using metadata associated with them.
The track metadata is kept in a CSV-format file, with any number of columns, and with a “label” column whose contents must correspond to the track labels in the JBrowse configuration.
The demo bundle contains an example trackMetadata.csv file, which can
be copied into the data directory for use with this configuration.
cp ../trackMetadata.csv data/
Then a simple faceted track selection configuration might look like:
"trackSelector": {
"type": 'Faceted',
},
"trackMetadata": {
"sources": [
{ "type": 'csv', "url": 'data/trackMetadata.csv' }
]
}
Then all we have to do is add this bit of json to the
jbrowse_conf.json file in the jbrowse directory:
gedit jbrowse_conf.json
(Copy and paste the above bit of json between the opening and closing curly braces (“{}”)).
Save it and refresh your browser, and you should now see the faceted track selector activated.
Tracks can be modified by changing several aspects of how the images are created. While this can be done be done both with HTML and Canvas tracks, this tutorial will focus on Canvas tracks only (the repeat tracks created above).
The configuration for the RepeatMasker track looks like this:
{
"type" : "CanvasFeatures",
"trackType" : "CanvasFeatures",
"style" : {
"subfeatureClasses" : {
"match_part" : "feature"
},
"className" : "generic_parent"
},
"compress" : 0,
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"label" : "repeatmasker",
"urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json",
"key" : "RepeatMasker"
},
Open the trackList.json file and locate this section of code:
gedit data/trackList.json
Control-F will open a “find” window in gedit; search for “repeatmasker”. A simple change we can make is to the color; in the line starting with “style”, add:
"color" : "black",
save the changes and select the RepeatMasker track or reload the browser to see the change. Many attributes of the display can be modified in this way, see the JBrowse Configuration Guide for a list of options.
Much like GBrowse’s perl callbacks that can change the track display, in the JBrowse configuration file you can include JavaScript functions to change the way tracks look. For example, in the RepeatMasker track, we can change the color of the glyph depending on what kind of repeat it is (where we happen to know that the type of repeat is encoded in the name). In this example, we leave the glyph black, unless it is a low complexity repeat, where we’ll color it red. A function to do that would look like this:
"color" : "function(feature) { var name = feature.get('Name'); if (name.match('Low_complexity') ) { return 'red'; } return 'black'; }",
When editing the trackList.json file directly in this way, the function has to go all on one line, but if we create an “include file” (not covered here) the function can have carriage returns in it. Replace the simple “color : black” section we just created in the configuration file with the function above, save the file and reload the browser page to see the changes (you might have to mouse around to find a low complexity repeat).
The default action when you click on a glyph is to open a “floating” window that displays everything JBrowse knows about a feature. If you’d like something else to happen, you have several options (outlined here), including having a different floating window open or executing any JavaScript function you define. For this example, we’ll create a link that will Google the repeat’s name and open the result in a new window. In the RepeatMasker section of the JBrowse configuration, we’ll add a section that looks like this after the style section:
"onClick" : {
"iconClass" : "dijitIconDatabase",
"action" : "newWindow",
"url" : "http://www.google.com/search?q={name}",
"label" : "Search for {name} at Google",
"title" : "function(track,feature,div) { return 'Searching for '+feature.get('name')+' at Google'; }"
}
If you’re having difficulties, the RepeatMasker section of the configuration file should now look something like this:
{
"type" : "CanvasFeatures",
"trackType" : "CanvasFeatures",
"style" : {
"color" : "function(feature) { var name = feature.get('Name'); if (name.match('Low_complexity') ) { return 'red'; } return 'black'; }",
"subfeatureClasses" : {
"match_part" : "feature"
},
"className" : "generic_parent"
},
"onClick" : {
"iconClass" : "dijitIconDatabase",
"action" : "newWindow",
"url" : "http://www.google.com/search?q={name}",
"label" : "Search for {name} at Google",
"title" : "function(track,feature,div) { return 'Searching for '+feature.get('name')+' at Google'; }"
},
"compress" : 0,
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"label" : "repeatmasker",
"urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json",
"key" : "RepeatMasker"
},
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.
Beginning 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 can display GFF3, BAM, BigWig, and VCF+Tabix files directly from your local machine without the need to transfer any data to the server. Just use the “File -> Open” tool from the menu bar to add tracks using local files.
Starting in version 1.10.0, users can define tracks that are combinations of the data in other tracks. The operations used to combine these tracks can be set operations (union, intersection, subtraction), arithmetic operations for quantitative tracks (addition, subtraction, multiplication, division), and/or masking operations to just highlight or mask some regions based on data in another track.
To add a combination track, select “File->Add combination track” from the menu bar, and drag existing tracks into the new combination track to start combining them.
If the old JBrowse is 1.3.0 or later, simply move the data directory from the old JBrowse directory into the new JBrowse directory.
See the accompanying slides (PDF)
Facts about “JBrowse Tutorial PAG 2015”
| Has topic | JBrowse + |