JBrowse User Guide

Setup and Configuration Documentation

  • JBrowse has a simple double pane interface, with the list of tracks on the left side and the display of features on the right. The navigation and search panel are located right below the menu bar.


    Moving
  • You can move across the genome by clicking and dragging your mouse inside the track window or by using the navigation tools or by pressing the left and right arrow keys on your keyboard.
  • Center the view at a point by clicking on either the track scale bar or overview bar, or by shift-clicking in the track area.
    Zooming
  • Zoom in and out by clicking zoom buttons in the navigation bar or by pressing the up and down arrow keys + shift. Select a region and zoom to it ("rubber-band" zoom) by clicking and dragging in the overview or track scale bar, or shift-clicking and dragging in the track area. Some tracks allow you to zoom into a feature as one of its right-click(CTRL+CLICK on MAC) drop down menu options.


    Displaying a Track
  • Turn a track on by checking its box.
  • Turn a track off by selecting the "X" button on the track header.

  • A drop down menu is available for each track.

  • Jump to a feature by typing its name in the location box and pressing Enter. You can also search by the gene symbol.
  • Jump to a specific region by typing the coordinates into the location box as: ref:start..end
  • The metadata that is available in the Faceted list selector is search/filter enabled as well.
  • The track list can be filtered using the text box.


Example Searches
uc0031k.2
searches for the feature named uc0031k.2.
chr4
jumps to chromosome 4
chr4:79,500,000..80,000,000
jumps the region on chromosome 4 between 79.5Mb and 80Mb.
5678
centers the display at base 5,678 on the current sequence

Track Lists

    Hierarchical Track List
  • The hierarchical track list displays tracks arranged into various categories and sub-categories.


    Faceted Track Displayer
  • In addition to the tracks available within the hierarchical menu, additional tracks are available through the faceted track displayer.
  • The comprehensive list of metadata are available on the left hand side and is searchable. The data displayed within the columns are only a subset.
  • The dual display of the hierarchical and faceted list is a plugin we have developed within the Araport project.This enables the capability to partition tracks, placing metadata rich tracks in the “Faceted” selector while using the default “Hierarchical” selector for everything else.

New Features

    SeqLighter v1.0
  • SeqLighter is a dynamic sequence viewer plugin implemented with the BioJS framework.
  • To launch the sequence viewer, right click((Ctrl+click on Mac) a gene model on the ‘Protein Coding Gene Models’ track. Select View Sequence on the drop down menu.

  • This will launch a popup screen displaying the nucleotide sequence of the selected gene model. The default format is in CODATA and there are other sequence formats such as FASTA, PRIDE, and RAW to choose from.

  • Flanking Sequence: An option to add upstream and downstream sequences of the gene model is available in 500bp, 1K, 2K, 3K and 4K.

  • When one of these are selected, the additional sequence is highlighted in grey.Note: The flanking sequences will not available in the downloaded image.
  • The downloadable formats include PNG, JPEG and SVG.
  • Note: The downloaded images will only be in CODATA format.
  • Highlighting options for exons, introns, utrs and start/stop codon is available. In addition, reverse complement of the selected sequence [including flanking regions] is available.




  • When reverse complement is enabled, other highlighting options will not be available. The highlighting is available for all of the sequence formats such as FASTA, PRIDE, CODATA and RAW.
    Variant Tracks Features
  • Select the 1001 Genomes track from the track list.



  • The 1001 Genomes variant track is color coded by the most severe variant consequence using Ensembl's consequence diagram.
  • The color legend is available on the track drop down menu.



  • The track can be filtered by the consequence variation type (missense, intron_variant, frameshift variants, etc):




  • The track can also be filtered by the variant type (deletion, insertion, snv, etc.):



  • To view the variant feature dialogue box, right click(Ctrl+click on Mac) a variant marker on the 1001 Genomes track and select "View Variation Feature from the menu.
  • The variant feature dialogue box retrieves the data using Ensembl's REST API.



  • The variation features popup displays genotype, population and phenotype data for the selected feature.



Future Developments

  • Feature list export to interact with Thalemine, BLAST and other Science Apps
  • Add filters for various tracks
  • Enable web services