User guide
Navigating the UI
Linear genome view usage
To start a linear genome view, use the menu bar
File->Add->Linear genome view
Using the location search box
- Use the search box in the LGV
- Enter syntax chr1:1-100 or chr1:1..100
- You can also specify an assembly name with the locstring {hg19}chr1:1-100
Note: searching by gene name is not yet available but will be added soon!
Scrolling
Mouse wheel can scroll side to side, as well as click and drag. The pan buttons also exist in the header of the linear genome view
Zooming
The zoom buttons exist in the header of the linear genome view, and there is also a slider bar to zoom in and out.
Note: You can also hold the "Ctrl" key and use your mousewheel or trackpad to scroll and this will zoom in and out
Re-ordering tracks
There is a drag handle on the track labels indicating by the six dots, clicking and dragging on this part of the track label can reorder tracks
Adding tracks
To add a new track or connection, you can use the menu bar in the app to open the form for adding a track:
File->Open Track
The \"Add track form\"
Note: There is also a circular "+" button inside the track selector menu that can also be used to access the "Add track" form.
The \"Add track button\" in the tracklist
In the "Add track" form, you can provide a URL to a file to load. Opening files from your local machine is not supported currently in the jbrowse-web app (jbrowse-desktop does allow this though, and may be added to jbrowse-web in the future)
Paste a URL to a file and optionally provide an index file URL too. The following file formats are supported
- Tabixed VCF
- Tabixed BED
- Tabixed GFF
- BAM
- CRAM
- BigWig
- BigBed
- .hic file (Juicebox)
For tabix files, TBI or CSI indexes are allowed. CSI or BAI is allowed for BAM. Only CRAI is allowed for CRAM. The index will be inferred for BAI or TBI files as filename+'.bai' for example, but if it is different than this, make sure to specify the index file explicitly.
Note: If you are an administrator, you can add tracks with the command line or with the admin server add-track or admin-server guide
Sharing sessions
The main menu bar has a "Share" button to enable users to share their sessions with other people. The share button generates a URL that can be sent to other users. It is not possible to copy your URL bar and send this to another user currently, because sessions can become too large for the address bar in many cases.
Note that you can copy and paste URLs between different tabs in your local browser though
The session URL will contain
- what views are on the screen, and settings for the views (e.g. track labels overlapping or offset)
- what tracks are in the view
- extra tracks that you added with the "Add track workflow"
- for the alignments track, the show soft clipping and sort settings on the pileup
- etc
All this stuff gets included in the session
This means you can share links with your custom tracks with other users, without being a JBrowse admin!
Editing track configs
Currently, in order to edit a track config, you have to make a copy of the track
Figure showing how to copy a track, note that settings button is disabled
because we don't \"own this track\" as a non-privileged user
After you have copied the track, you can edit the track settings
Figure showing the settings button is now enabled on the session track, and you
have full control over your session tracks
Your new track is a so-called "session track" and can be shared with other users with the "Share" button
Rubberband selection
The scale bars accept a click and drag action to select a region
Rubberband selection can be performed on both the region and overview scale bars
Track label positioning
Track labels can be positioned on their own row or overlapping the data to save vertical screen space. They can also be hidden. This is done by clicking on the hamburger menu for a specific view.
Example of using the overlap and offset track label positioning options
Horizontally flip
The view can be horizontally flipped, or reverse complemented, to make the coordinates go from right to left instead of left to right
We use triangles pointing in the direction of the orientation in the overview bar to help indicate whether the app is horizontally flipped or not
Here is an example of before and after horizontally flipping the view
Before and after horizontally flipping
Alignments tracks
Visualizing alignments is an important aspect of genome browsers. This guide will go over the main features of the "Alignments track"
The alignments track is a combination of a pileup and a coverage visualization
Pileup visualization
The pileup is the lower part of the alignments track and shows each of the reads as boxes positioned on the genome.
By default the reads are colored red if they aligned to the forward strand of the reference genome, or blue if they aligned to the reverse strand.
Coverage visualization
The coverage visualization shows the depth-of-coverage of the reads at each position on the genome, and also draws using colored boxes any occurrence of mismatches between the read and the reference genome, so if 50% of the reads had a T instead of the reference A, half the height of the coverage histogram would contain a 'red' box
Screenshot showing the alignments track, which contains both a
coverage view at the top and a pileup view at the bottom
Show soft clipping
If a read contains bases that do not map the the genome properly, they can either be removed from the alignment (hard clipping) or can be included, and not shown by default (soft clipping)
JBrowse 2 also contains an option to "show the soft clipping" that has occurred. This can be valuable to show the signal around a region that contains structural variation or difficult mappability
Shows what turning on soft-clipping enables for a simulated long-read
dataset. There is a simulated structural variant, a deletion, at this position,
so the read has bases that map to the other side of the deletion being revealed
by this.
Sort by options
The alignments tracks can also be configured to "sort by" a specific attribute for reads that span the center line.
By default the center line is not shown, but by showing it (Go to the view's hamburger menu->Select "Show center line") then you will obtain a better idea of what the "sort by" option is doing
Showing the center line
Here is how to turn on the center line
- Open the hamburger menu in the top left of the linear genome view
- Select "Show center line"
Illustrates before and after turning on the center line. The center line is an
indicator that shows what base pair underlies the center of the view. Note that
this is used in the \"Sort by\" option discussed below; the sort is performed
using properties of the feature or even exact base pair underlying the center
line
Sorting by base
Sorting by base will re-arrange the pileup so that the reads that have a specific base-pair mutation at the position crossing the center line (which is 1bp wide) will be arranged in a sorted manner. To enable Sort by base
- Open the track menu for the specific track using the vertical '...' in the track label
- Select 'Sort by'->'Base pair'
Illustrating the pileup re-ordering that happens when turning on the Sort by->Base pair. The sorting is done by specifically what letter of each
read underlies the current center line position (the center line is 1bp wide,
so sorted by that exact letter)
There are other sorting options available and more to come. If you have any requests please drop us a line via github here
BigWig tracks
Visualizing genome signals, whether it is read depth-of-coverage or other signal, can often be done by using BigWig files
This figure shows a BigWig using the XY plot renderer
Line plot version of a BigWig
There are many options for controlling the BigWig which can be accessed from the UI. See the bigwig configuration guide
Linear synteny and dotplot views
The dotplot view is a 2D comparative view that can display alignments between different genome assemblies, or even compare a long-read or NGS short-read versus the genome
Opening a dotplot view
Currently the workflow for launching a dotplot is done by navigating in the header bar to the File->Add->Dotplot view
This will let you select the genome assemblies of interest
Then you can also provide a synteny file in the form of PAF via the Add track workflow
Then currently you must configuration edit the PAFAdapter to indicate the two assemblies in the PAFAdapter
Adding a new dotplot or synteny view via the menubar
Example of the import form for a dotplot or synteny view. Allows you to select
two different assemblies and a PAF file can be supplied via a URL
Example of a dotplot visualization of the grape vs the peach genome
See the dotplot configuration for more detailed descriptions
Opening a linear synteny view
Use the main menu bar to select
File->Add->Linear synteny view
Adding a new linear-synteny-view via the menubar
Example of the import form for a synteny view allowing you to select two
different assemblies and optionally adding a PAF file via a URL
Figure showing grape vs peach synteny
See the linear synteny configuration for more details on manually configuring the synteny view
Long read vs reference plots
One can also launch a dotplot view that compares a long read to the reference genome by
- Right clicking an alignment
- Select "Dotplot read vs ref" or "Linear read vs ref" in the context menu
Example of a dotplot of a long read vs the reference genome
Example of a \"synteny\" view of a long read vs the reference genome
Hi-C tracks
Visualizing Hi-C data can be performed with .hic files which are generated by the Juicebox software suite. It uses the hic-straw module developed by the juicebox/igv.js team to visualize it in jbrowse.
Currently configuration options are basic for Hi-C tracks, see configuration for info about configuring Hi-C
tracks
Screenshot showing a Hi-C track
SV inspector
The SV inspector is a "workflow" that is designed to help users inspect structural variant calls
Opening the SV inspector
We can start the SV inspector by launching it from the App level menu bar
The SV inspector can be launched from the main menu bar
This will bring up an "import form" that asks you for your SV evidence. This can be provided using a URL in these formats:
- VCF (plain text VCF, not tabix VCF)
- BEDPE
- STAR-fusion result file
- or other formats
SV inspector import form
Example SV inspector workflow
We can start the SV inspector workflow by opening up this file containing translocation events called from a breast cancer cell line SKBR3, based on these published data http://schatz-lab.org/publications/SKBR3/
Copy this URL and paste it into the import form and select hg19
SV inspector import form with URL
SV inspector results
After loading the user's requested file, you will have a spreadsheet with each row representing a row of the file you opened, along with a whole-genome overview of the SVs on the right
SV inspector with loaded results
Now here is where things can become interesting
We can perform searching and filtering on the table, which can filter down the number of rows being displayed, and then this dynamically filters the circos view on the right also.
SV inspector with filter applied
Launching breakpoint split view
By clicking on the features in the Circos, or clicking on the triangle drop-down on the leftmost column of the spreadsheet, we can dynamically launch a new view of the data that is called the "split view" or the "breakpoint split view"
This allows us to inspect the breakpoints of the structural variant, and compare each side to the alignments.
Variant tracks
Visualizing variant tracks from the VCF format alongside the original alignment evidence track is a common workflow for validating your results. In JBrowse 2 we can open a variant track and an alignments track as shown below
Variant track indicating a SNP alongside the alignment track evidence
Variant widget
The variant features have a specialized widget that contains a table indicating all the calls that were made in a multi-sample VCF. Some VCF files, like the 1000 genomes VCF, can contain thousands of samples in a single file. This table can display the details
Future additions
We anticipate adding more features to the variant track in the future including
- Ability to visualize individual samples in a multi-sample VCF as subtracks of a variant track
- Ability to use FILTER the VCF column via the track menu