Genome Browser
CapBase genome browsers use JBrowse to display genome assemblies and annotation tracks for C. rubella, C. orientalis, and C. grandiflora.
Browser Pages
View a Region
Go to a species-specific Genome Browser page > Enter a chromosome, coordinate, or locus ID > Open the region > Turn on tracks for inspection.
Searching for a Region or Locus
Users can jump to a feature, reference sequence, or genomic interval by typing into the genome browser location box and pressing Enter.
Jump to a Feature or Reference Sequence
Type the feature name or reference sequence name in the location box > Press Enter.
Jump to a Specific Region
Use one of these formats:
ref:start..endref:start-end
Commas are allowed in start and end coordinates. For example:
lcl_Cr_6:100,000..200,000
Open Multiple Regions or Chromosomes
A space-separated list of location strings can be used to open multiple chromosomes or regions at once. For example:
lcl_Cr_6 lcl_Co_6 lcl_Cg6.2lcl_Cr_6:1-100 lcl_Co_6:1-100
Open a Region in Reverse Orientation
Add [rev] after the region. For example:
lcl_Cr_6:1-100[rev] lcl_Co_6:1-100
Use Whitespace-Separated Reference Name, Start, and End
For example:
lcl_Cr_6 100 200
If a feature cannot be found, check whether the locus ID or chromosome name matches the selected species. For more solutions, visit the Troubleshooting page.
Example Browser Searches
| Example input | What it does |
|---|---|
Cr1G00010 | Searches for the feature named Cr1G00010 in C. rubella |
lcl_Cr_6 | Jumps to the C. rubella chromosome/reference sequence lcl_Cr_6 |
lcl_Cr_6:100,000..200,000 | Jumps to the region on lcl_Cr_6 between 100 kb and 200 kb |
lcl_Cr_6:1-100 lcl_Co_6:1-100 | Opens a split view of lcl_Cr_6:1-100 and lcl_Co_6:1-100 |
lcl_Cr_6 lcl_Co_6 lcl_Cg6.2 | Opens multiple chromosomes/reference sequences at once |
lcl_Cr_6:1-100[rev] lcl_Co_6:1-100 | Opens the first region in reverse orientation and the second region normally |
lcl_Cr_6 100 200 | Uses whitespace-separated reference name, start, and end |
Preloaded Tracks
CapBase genome browsers include several preloaded tracks for each species. These tracks provide reference genome sequences, gene annotations, repeat annotations, and transposable element subtracks.
| Track name | Type | Description |
|---|---|---|
| Reference sequence | Genome assembly | Reference genome sequence for the selected species. |
| Gene annotation | Gene model annotation | Protein-coding gene and transcript annotation. |
| Repeats annotation | Repeat annotation | Full repeat annotation, including TE and non-TE repeat features. |
| Non-TE repeats | Repeat subtrack | Non-transposable-element repeat features. |
| TE only | TE subtrack | Transposable element annotations only. |
| Class I retrotransposons | TE subtrack | Retrotransposon annotations. |
| Class II DNA transposons | TE subtrack | DNA transposon annotations. |
| LTR | TE subtrack | Long terminal repeat retrotransposon annotations. |
| LINE | TE subtrack | Long interspersed nuclear element annotations. |
| SINE | TE subtrack | Short interspersed nuclear element annotations. |
| RC/Helitron | TE subtrack | Rolling-circle/Helitron transposon annotations. |
| TIR transposons | TE subtrack | Terminal inverted repeat transposon annotations. |
Adding Custom Tracks
Users can add their own local or remote data tracks to JBrowse for visualization alongside CapBase annotations. Custom tracks are for browser visualization and are not permanently uploaded to or stored by CapBase.
Open the Genome Browser > Open the File or Add track menu, depending on the JBrowse interface > Choose a local file or provide a remote URL > Select the correct data format > Add the track > Turn on the track in the track selector.
For large files, indexed formats are recommended for smoother browsing. If an indexed format is used, make sure the data file and its index file are accessible together.
Supported Data Formats
- BAM / CRAM
- htsget
- VCF, Tabix-indexed or plain text
- GFF3, Tabix-indexed or plain text
- BED, Tabix-indexed or plain text
- BigBed
- BigWig
.hicHi-C contact matrix- CSV, TSV, BEDPE, and STAR-fusion output for tabular view
If the browser is blank or a track does not load, visit Troubleshooting.
Exporting Browser Views and Track Data
Users can export visual browser views and track-related information from JBrowse when supported by the interface.
Export a Screenshot
Open the Genome Browser > Navigate to the region of interest > Turn on the desired tracks > Open the Export or Screenshot option in the JBrowse menu > Save the image.
Screenshots are useful for presentations, reports, and quick visual summaries.
Export Track Data
Open the Genome Browser > Select or open the track of interest > Use the available Export, Download, or track menu options > Save the selected data if the track supports export.
Available export options may depend on the track type and the JBrowse interface.
Learn More
For more detailed instructions on JBrowse features, track configuration, supported data formats, and advanced usage, visit the official JBrowse 2 documentation.