Contributed tracks are annotations produced by research groups and integrated into the default Genome Browser view on GenArk assemblies. This page describes how to prepare and submit them.
Each assembly gets its own subdirectory named by its NCBI accession identifier (GCA_ or GCF_). Data files and the trackDb.txt must use the same file names in every assembly directory. This allows a single trackDb.txt to work across all assemblies.
+-- hub.txt +-- genomes.txt +-- documentation.html +-- GCA_000260495.2/ | +-- trackDb.txt | +-- myTrack.bb | +-- myTrackDocs.html +-- GCF_014441545.1/ | +-- trackDb.txt | +-- myTrack.bb | +-- myTrackDocs.html +-- GCF_014108235.1/ | +-- trackDb.txt | +-- myTrack.bb | +-- myTrackDocs.html
hub myProjectHub shortLabel My Contributed Tracks longLabel Contributed annotation tracks for GenArk assemblies email user@example.edu genomesFile genomes.txt descriptionUrl documentation.html
The descriptionUrl page provides an overall description of the hub or research project. For details on hub.txt settings, see the Track Hub User Guide.
genome GCA_000260495.2 trackDb GCA_000260495.2/trackDb.txt genome GCF_014441545.1 trackDb GCF_014441545.1/trackDb.txt genome GCF_014108235.1 trackDb GCF_014108235.1/trackDb.txt
One block per assembly, separated by a blank line. The genome value is the NCBI accession identifier, and trackDb points to the trackDb.txt file in that assembly's subdirectory.
track myTrack shortLabel My Track longLabel My contributed annotation track for GenArk assemblies type bigBed 9 + visibility dense bigDataUrl myTrack.bb searchIndex name html myTrackDocs
Because data files have the same name in every assembly directory, this identical trackDb.txt works for all assemblies. The bigDataUrl is a relative path to the data file in the same directory. The html setting points to the track documentation page (without the .html extension). For the full list of trackDb settings, see the trackDb documentation.
Every track must have an HTML documentation page. Place it in each assembly directory with the filename referenced by the html setting in trackDb.txt (e.g., myTrackDocs.html). If you omit the html setting, the browser looks for [trackName].html in the same directory as the trackDb.txt file.
Structure your documentation page with these sections:
A template documentation page is available as a starting point. For an example of a completed track description, see the recombination rate track page.
An example contributed track hub with EVA SNP Release 8 data on five GenArk assemblies is available for reference:
Once your hub is ready, contact the UCSC Genome Browser team with your hub.txt URL. You can test it first by loading it via My Data > Track Hubs in the browser. The team will review your submission and work with you to integrate the tracks.
For general information about track hubs, see the Track Hub User Guide. For best practices, see the Public Hub Guidelines.