FlyBase:JBrowse

JBrowse

JBrowse was developed and is maintained by the Generic Model Organism Database (GMOD) consortium.

Brief description of the JBrowse view

A typical JBrowse view has the following features

1. Available Tracks panel on the left for selecting tracks to be displayed in the genome viewer.
2. Genome viewer on the right with the following layers
   • File, View, and Help drop down menus along the top and as well as option to share screen at the far right.
   • Chromosome coordinate scale at the top with slider to move to different chromosome regions.
   • Scroll, zoom, search panel that allows for facile moving to the desired chromosome region. To the right of this is a highlight selector allowing a region of the genome view to be highlighted in yellow
   • Coordinate scale of the chromosome region in the viewer
   • Track-viewing region

Navigating around the genome

Choosing a genome

D. melanogaster is the only genome available for viewing with JBrowse in FlyBase.

Displaying a specific region of the genome

To select a specific region of the genome to view, enter a symbol, FlyBase ID, or sequence location in the coordinate box at the top of the JBrowse view.

Navigating with a symbol, e.g. Act5C, cnn

1. Enter a symbol in the box, e.g. Act5C. As you start to enter a value, the autocomplete feature will offer valid FlyBase symbols that match the input value.
2. Select a value from the dropdown menu.
3. Click on “Go”
4. A popup box will appear with matching values. Choose to “show” (bring up the region in the JBrowse viewer) or “Go” (bring up the region and dismiss the selection box).

Navigating with an ID

1. Enter an ID in the box, e.g. FBgn0000577. As you start to enter a value, the autocomplete feature will offer valid FlyBase IDs that match the input value.
2. Select a value from the dropdown menu.
3. Click on “Go”
4. The view will shift to the region of interest.

Navigating with a sequence location

1. Enter a sequence location, e.g.

   2R:11,524,006..11,528,210

   3R:19044882..19094270

   2R:11,524,006..11,528,210 [-] (copied straight from the Sequence Location field in a FlyBase gene report)

2. Click on “Go”
3. The view will shift to the specified region.

Zooming

To view a subregion of the region already displayed, select a smaller region by clicking and dragging along the lower coordinate scale. The view will immediately shift to the selected region.

Alternatively, use the “-” and “+” icons in the upper left corner to zoom the view in and out.

Moving across the genome

There are two ways to move laterally along the genome:

Scroll left or right with the left and right arrow buttons at the top left. The view will shift by nearly the extent of full screen (such that if you are scrolling to the right, the features initially seen on the right-hand border will shift to the left-hand border). Panning - position the mouse over an "empty" region of the JBrowse image, and click and drag left/right to pan across the genome.

To jump to a different section of the chromosome, click on the chromosome coordinate scale at the top of the view. The region of the chromosome that is currently displayed in the detail panel is indicated with two red lines.

Centering

Click on the coordinate scale to recenter the genome viewer around the location you clicked.

Customizing the display

Changing the order of the tracks

To change the order of the tracks in the display panel click on the Track Title and drag up or down.

Selecting data tracks

Available Tracks are organized into various sections which can be collapsed or expanded with the arrow at the left:

• Reference Genome
• Aligned Evidence
• Mapped Mutations
• Noncoding Features
• Similarity (Orthologs)
• RNAi Reagents and Data
• Aberrations
• Expression Levels (RNA-Seq)
• Expression Levels (Small RNA-Seq)

To add a new track to the genome view, click on the track name in the Available Tracks panel at the left of the screen.

To remove a track, click on the “x” in the track label panel in the genome viewer or deselect in the Available Tracks panel. For details on individual tracks see JBrowse Tracks.

Note that newly selected tracks always appear at the bottom of the JBrowse viewer and can be rearranged by clicking on the track name and dragging to the desired position. Only one track can be moved at a time. With a few exceptions, including resets occurring with new FlyBase releases, track selections are preserved from session to session.

Track options for saving to a file, deleting and compressing

Several options are available in the drop-down menu at the right hand side of many of the track labels in the genome viewer.

Pin to top - keeps the track at the top of the view

Delete track - deletes the track from the genome viewer and from the “Available Tracks” menu. (Use the refresh button to restore any default tracks that you may have deleted; it will not restore any custom tracks you have added).

Save track data - the track data for the visible region or the whole chromosome arm or scaffold can be saved as GFF3, BED, or Sequin Table. Select the region to be saved, the desired format, specify a file name, and then view the data in a pop-up window or save to a file.

Display mode - you can choose a normal, compressed, or compact view for tracks from the “display mode” drop-down menu.

Show labels - toggle on and off the track labels

Adding custom tracks

To add custom tracks go to the “File” drop-down menu at the top and select “Open track file or URL”

Open sequence file

Select "Open sequence file" from the “File” drop-down menu at the top left of the viewer.

Other useful features

Sharing as a URL

JBrowse views can be saved and shared as a URL. Click on the “Share” button in the top right corner of the screen. The provided URL can be copied and shared via email or other medium.

Ruler

Clicking on the bottom coordinate scale brings up a vertical red line that can be dragged across the JBrowse display and used to gauge the relative positions of features in different tiers. The coordinate corresponding to the position of the line is displayed at the top.

Links to report pages

Clicking on a gene brings up a pop-up with a computed summary of gene information and links to the FlyBase and NCBI reports. Clicking on most genomic features displayed in the GBrowse genomic viewer leads to a detailed report of curated information connected to that feature; reports on the relevant alleles, insertions, aberrations, and sequence features can be accessed in this way. cDNAs and ESTs link to GenBank sequence accession reports.

Highlight a Region

Click on the “HIghlight a Region” icon that looks like a yellow marker to the right of the coordinate box. Drag the cursor laterally along the genome viewer to select a region. The region will be highlighted in yellow. Click the icon again to remove the highlighting.