The JBrowse Genome Browser


The JBrowse interface is primarily focused on the browser itself, allotting much less space to the menu and header regions. As such, the menu/search/navigation area has been substantially consolidated compared to the GBrowse browser. Although this results in a "look and feel" that is quite different, closer examination will reveal that much of the data and many of the navigational tools are shared between the browsers.


For more about individual JBrowse tracks, click here.

Click here to go to the JBrowse tool.


A Quick Guide to Using JBrowse


Selecting a map/assembly in JBrowse

The menu bar at the top of the window includes the dropdown to select a genome assembly. RGD currently has JBrowse instances for rat genome assemblies RGSC 3.4, RGSC 5.0 and RGSC 6.0; mouse build 37; and human builds 36.3 and 37.
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The JBrowse Search Box

The JBrowse search box is located between the lines for the chromosome-level position and the detail-level position (see "Navigation" below) in the consolidated header region. Autocomplete, which offers suggestions based on what you have already typed, is included for object symbols.  For example, typing Ucp results in a list which includes the gene symbols Ucp1, Ucp2 and Ucp3, as well as the marker symbol "Ucp2_Ucp3"

Alternatively, the position may be entered as Chr#:start..stop, for example Chr1:171,707,625..171,713,991.  Commas can be used as thousands separators in the start and stop nucleotide position numbers but they are not required.

Selecting a different chromosome number in the dropdown to the left moves the selection to the same nucleotide position on a different chromosome.

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Selecting Tracks in JBrowse

Track selection is conveniently located as a list of available tracks in the left side bar. Tracks are divided into categories and, in some cases, subcategories. Categories appear on a grey background. The number of tracks in that category is shown to the right of the category name. The default is to show all the categories "collapsed" to give an overview and minimize scrolling. (Depending on the speed of your computer's processor, you may actually see the categories collapse when you first open the tool.  This is normal.) A right-pointing arrow to the left of the category or subcategory name indicates that the menu is closed. Click the name of the category to open the section and display either the subcategories or the individual tracks beneath it. Track names are shown on a white background and have a check box beside the track name.

Click the check box to the left of the track name to turn that track on.  Click again (i.e. uncheck the box) to turn it off. As tracks are turned on, they will appear at the bottom of the browser display. Tracks in the browser display can be reordered by dragging the name of the track in the display (not in the list of available tracks) to the desired location and "dropping" the track there.

There is a "filter" box at the top of the list of available tracks. Enter a term, such as "cardiovascular" in this box to reduce the available tracks to those matching your term (i.e. tracks where the term you enter appears in the name of the track). In the example to the left, only three of the "Disease Related Tracks", the "Cardiovascular Diseases Related" Genes, QTLs and Strains tracks, include the word "cardiovascular" in their names. Notice that the other categories are still visible in the list but the number following the category name is "0" indicating that none of the tracks in that category match the filter criteria. Click the red "X" beside the filter box to remove the term and restore all the tracks to availability.

For more information about individual tracks, click here.
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Navigation in JBrowse

The Chromosome-level and Detail-level Position Bars

The upper grey bar in the tool header gives the chromosomal position being shown in the detail display as a red vertical line or box. The lower gray bar at the bottom of the header region gives the chromosomal positions of the detail display below it. Light blue shading connects the ends of the outlined area in the chromosome view to the ends of the detail view below.

The Navigation Buttons

Navigation buttons are located to the left of the search box in the consolidated header region.  As with GBrowse, the arrow buttons move the view about the distance of one screen left or right.  The larger zoom buttons zoom in or out about twice as far as the smaller buttons.

In addition to these buttons, JBrowse supports click and drag selection of regions in both the chromosome-level and detail-level position bars (see #5 and 6 on the GBrowse to JBrowse comparison page).

To move the region displayed in the browser a short distance to the left or right, you can also click in an unoccupied area of the browser window and hold the mouse button down while dragging the display in the direction you would like it to go.

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Context-specific Menus for JBrowse Tracks

The context-specific menus for data tracks are accessible, but hidden by default.  Click the down arrow on the title bar of the track to access menu options for changing the way the track is displayed and exporting data for that track.

About this track:  "About this track" gives some additional information about a particular track such as the track type and category.

Pin to top:  "Pin to top" causes that track to always be displayed directly beneath the header area at the top of the browser window.  By default tracks are displayed in the order they are turned on but they can be re-ordered by clicking and dragging the track title bar up or down.  When a line appears in the place you want the track to appear, release the mouse button and the track is dropped in that location.

Edit Config:  "Edit Config" allows the user to directly edit the configuration script for a particular track.  This is not recommended for most users.  However, it is possible to use this function to change the height of the track if not all of the data is showing using the default settings.  Click here for more information.

Delete track:  Individual tracks can be turned off in three ways:  by selecting "Delete track" in the context-specific menu, by clicking the X to the left of the track name, or by unchecking the box in the "Available Tracks" list in the side bar of the browser window.

Save Track Data:  "Save Track Data" opens a popup window with options for viewing and/or saving the data for a particular track.  For more information about saving track data, see below.

Display mode:  Three display modes are available:  "Normal" is the default view.  "Compact" reduces the height of each object in the track and turns off the display of object labels so that the height of the track is proportionally reduced even though each object can still be seen separately.  "Collapse" moves all objects to a single line on the track which in some cases results in overlap of individual objects.

Show labels:  Object labels are automatically displayed when the view is zoomed in sufficiently.  Uncheck the "Show labels" box to turn them off.

More about saving track data:

"Save Track Data" opens a popup window with options for viewing and/or saving the data for a particular track. Two options are available:  to save the data just for the particular region you are viewing or, for some tracks, to save all the data for that track for the particular chromosome that you are viewing. However, the latter option is not available for large datasets such as the strain-specific variant tracks. (For this data, RGD has vcf files available on our ftp site.) In the "Save Track Data" popup select a file format, edit the name of the file, if desired, and choose whether to simply view the file online or save it to your local system.
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Highlighting a Region in JBrowse

JBrowse supports highlighting a region, not an object. However, if you know the position of the object you are interested in (for example, from an RGD report page), you can use the View-->Set Highlight function in the dark blue menu bar at the top of the page. Enter the position in the popup window as Chr#:start..stop just as you would enter a region in the JBrowse search box. Click the button labeled "Highlight" and the region you entered will be highligted in yellow across all the open tracks. Be aware, if the position you enter is not in the region that is being shown in the browser, the region you specify will be highlighted but you will not see it (i.e. the browser will not move to the highlighted region). If, however, you navigate to that region it will be displayed with the yellow highlight.
You can also highlight a region in the browser using the "Highlight a region" button to the right of the search box. Click this button, then click and drag in the browser window to select the region to highlight. Do not click and drag on the position bar for this function. Doing so will cause the browser to zoom to that region, not highlight it. Once a region is highlighted, it will remain highlighted through movements, zooming, etc. To clear the highlighting, go to View-->Clear Highlight to remove the yellow highlighting. Only one region may be highlighted at a time. Selecting a second region to highlight removes the highlight from the first region rather than adding to it.
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How to obtain FASTA sequence for a region using JBrowse

JBrowse can be used to extract genomic sequences for limited regions. Navigate to your region of interest and turn on the sequence track. For RGSC 5.0, for instance, this is found in the "Reference Data" category under "Sequence". The track name is "rn5 DNA". Unless you are viewing a very small segment (e.g. approximately 550 bp or less), the track will display a message saying you should zoom in to view the sequence in the browser. However, even when this message is displayed, you can still view and save the FASTA sequence using "Save Track Data". Click the down arrow to the right of the track name and select "Save Track Data". The image to the right shows an example in which the sequence for a region of approximately 11 kb was viewed, downloaded and saved, despite the fact that the browser track showed the "Zoom in to see sequence" message.

For more about the Reference Sequence track in JBrowse, click here.

For more about saving data from other kinds of tracks, click here.

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Sharing a JBrowse View


In the top right corner of the JBrowse window (at the right side of the blue menu bar), is a button labeled "Share". Click this button to obtain a URL that can be copied and pasted into a new browser window, or into a document, email, instant message, etc. to give access to the same view, i.e., the same region with the same tracks open in the same order. The URL does not go to an image of JBrowse, rather it opens the browser itself so the recipient can manipulate the tracks and region as needed.
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What's New in JBrowse

Strain-specific Variant Track Placement


Strain-specific variant tracks are not new in JBrowse, but their placement in the "Available Tracks" menu is different than where they appeared in the GBrowse "Select Tracks" menu. The strain-specific variant (SSV) tracks have been incorporated into the general "Variants" category. In addition, all of the SSV tracks appear in a single list rather than being separated by sequencing institution. This makes finding a strain's variants easier to find. Because the strains are listed in alphabetical order by the strain symbol, followed by the abbreviation for the sequencing institution, cases where the same strain or substrain have been sequenced by multiple groups appear together, simplifying comparisons.

For more information about the strain-specific variant tracks, click here.

RNA-Seq BAM Alignment Tracks

JBrowse marks the introduction of RNA-Seq data into RGD's genome browsers. A complete set of BAM alignments between RNA-Seq reads and the RGSC5.0 reference genome sequence are available for a study of Hypoxia in BN and SS rats by the Lazar/Jacob group at MCW. The size of this data makes it impossible to display in GBrowse, whereas JBrowse is far more scalable and able to handle large datasets without slowing down.

For more information about RNA-Seq BAM alignment tracks in JBrowse, click here.

Gene Predictions Based on RNA-Seq Data

The JBrowse for v5.0 also includes a set of gene predictions based on RNA-Seq data with and without the addition of ESTs, from the Liu lab at MCW. These tracks display the gene predictions based on RNA  sequencing of bone marrow, brain and kidney, highlighting differences in expression between these three diverse organs.

For more information about tracks in JBrowse that show RNA-Seq based gene predictions, click here.

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