JBrowse is freely available without logging in to navigate through the genome and view tracks, but not to view user-submitted annotations or access the gene editing functions. Simply select a genome assembly under "JBrowse" to get started.
To access genome annotation editing functions and view user submissions, use the Apollo Registration pulldown menu to register for an account. Once you have login credentials, select a genome in the JBrowse pulldown menu. Then login with your credentials using the "Login" link located at the upper right side of the JBrowse browser.
Navigating the Genome
Once the JBrowse page is loaded for the first time, you will see a blank viewer with number lines and navigation controls at the top of the page. The upper number line represents coordinates of an entire chromosome, and has a red rectangle showing the specific location of the current view. The lower number line represents the chromosomal coordinates of the current view. Arrow buttons allow panning left and right, and zoom levels can be adjusted using the plus and minus icons. To the right of the zoom buttons is a pulldown menu to select a chromosome or scaffold, and a box to enter chromosome coordinates. Rather than selecting a chromosome and entering coordinates, you can enter a gene symbol or Ensembl/RefSeq gene/transcript id to navigate directly to its genome location. When there is more than one feature matching the search text, a table will appear allowing you to select one.
Selecting Tracks
Use the "Select Tracks" tab in the upper left corner of the browser to access the Faceted Track Selector which allows you to find tracks based on data type and various other attributes. Highlighting one or more categories on the left panel filters rows in the table on the right, which provides metadata for RNA-seq, such as tissue, BioSample accession and BioProject. In addition, the RNA-seq track name includes the SRA experiment accession. The table is further searchable by entering text in the “Contains text” search box above the table. Tracks are selected for viewing by clicking boxes to the left of the table.
Track Descriptions
Gene Prediction Tracks
Gene prediction tracks are provided for RefSeq and Ensembl genes, and display transcripts, including protein-coding, long non-coding and other RNA. Protein-coding gene tracks are configured to show untranslated regions (UTR) in dark blue. The coding portions of the exons are slightly thicker than the UTR, and appear in different colors representing reading frames. An arrow at one end of the transcript indicates coding direction, pointing right for coding on the plus strand, and left for coding on the minus strand. When zoomed out, gene prediction tracks appear as histograms depicting gene density, while zooming in allows the visualization of predicted introns and exons. Right clicking a transcript feature provides more information, which may include gene symbol, description and database cross references.
Gene Prediction Problem Tracks
The Ensembl Protein Coding Discordant track shows Ensembl protein coding genes that are either split or merged compared to RefSeq genes, or do not have corresponding RefSeq genes.
The RefSeq Protein Coding Discordant track shows RefSeq protein coding genes that are either split or merged compared to Ensembl genes, or do not have corresponding Ensembl genes.
RNA-seq Tracks
BAM dense tracks are useful for checking the suitability of a RNA-seq experiment for solving a particular gene prediction problem prior to zooming in with a more computationally intensive draggable BAM track. Right clicking an individual read alignment reveals additional information such as the read sequence and quality, alignment score, and details about matches, mismatches and indels in CIGAR format.
BAM draggable tracks are very computationally intensive, and require a sufficient zoomed-in level to avoid an error message. The name “draggable” refers to an Apollo feature, in that you can drag a single read alignment to the Editing Area to initiate an annotation. Right clicking an individual read alignment reveals additional information such as the read sequence and quality, alignment score, and details about matches, mismatches and indels in CIGAR format.
RNAseq junctions (arcs) tracks collapse junctions from individual reads for viewing when zoomed out to see entire genes or regions between genes. Arc thickness is related to the number of reads supporting the splice junction.
RNAseq junctions (flat) tracks collapse junctions from individual reads into a single bar. Right clicking an individual junction reveals additional information such as the number of reads that support the junction (the “Score”) and the start end end coordinates of the junction. These tracks are useful for confirming edges of exons, by ensuring that the junction start or end coordinate abuts the exon boundary.
StringTie tracks show transcripts models created by assembling RNA-seq read alignments, and can reveal the possibility of new isoforms. The tracks are similar in appearance to gene prediction tracks, but they do not distinguish UTR from coding regions. Similar to gene prediction tracks, StringTie tracks appear as histograms depicting density when zoomed out, and as intron/exon structures when zoomed in. Right-clicking an individual StringTie transcript shows additional information, including read coverage, FPKM and TPM.
XYPlot tracks show read depth in log scale, and are used to identify regions of high or low expression.
Repeats
RepeatMasker tracks were created using RepeatMasker (Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-4.0. 2013-2015) after identifying repeats using RepeatModeler. Repeat features are labeled with a name, and right clicking the feature shows the repeat class and family.
Variation Tracks
The SNP track shows variants from the European Variation Archive RS Release 4. Right clicking a variant feature shows the alternate and reference alleles.