-Researchers are creating annotations for hundreds of assemblies -in one process, or creating a number of annotations for one assembly. -It would be useful to the wider research community to have these -annotations included in the default browser view on those assemblies. +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.
--This discussion outlines procedures for submitting a set of tracks to the -browser for inclusion in the default view of a genome assembly. - This procedure is for developers of tracks that have a number of tracks -to submit to one assembly, or a set of tracks to deliver to a multiple -set of genome assemblies. -
+-Development process: -
+-- hub.txt +-- genomes.txt -+-- documentation.html +-- GCA_000260495.2/ | +-- trackDb.txt -| +-- veupathGenes.bb -| +-- veupathGenes.gtf.gz +| +-- myTrack.bb +| +-- myTrackDocs.html +-- GCF_014441545.1/ | +-- trackDb.txt -| +-- veupathGenes.gtf.gz -| +-- veupathGenes.bb +| +-- myTrack.bb +| +-- myTrackDocs.html +-- GCF_014108235.1/ | +-- trackDb.txt -| +-- veupathGenes.gtf.gz -| +-- veupathGenes.bb +| +-- myTrack.bb +| +-- myTrackDocs.html
-Assembly names need to be the NCBI GenBank accession names to -identify the corresponding assembly. GCF_... or GCA_... -
-All annotations must have appropriate documentation.
-The track hub directory structure must be as described here.
--hub PAG_2026_GenArk_Contrib_Example -shortLabel PAG 2026 GenArk tracks -longLabel PAG 2026 example of contributed tracks to UCSC GenArk assemblies -email genome@soe.ucsc.edu +hub myProjectHub +shortLabel My Contributed Tracks +longLabel Contributed annotation tracks for GenArk assemblies +email user@example.edu genomesFile genomes.txt descriptionUrl documentation.html - -# comments: -# load this hub with a reference to this hub.txt file: -# https://genome-test.gi.ucsc.edu/~hiram/BRC/contrib/hub.txt - -# for example, to show this track hub in the genome browser:: - -# https://genome.ucsc.edu/cgi-bin/hgTracks?genome=GCA_000260495.2& -# hubUrl=https://genome-test.gi.ucsc.edu/~hiram/BRC/contrib/hub.txt+
-The genomes.txt file specifies the target assemblies. -The descriptionUrl link refers to documentation.html for -this track hub. Since the data is uniform for all the tracks, -a single documentation.html can be sufficient for all documentation. +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+
-List each assembly for which you have calculated annotations. -The trackDb.txt file defines the tracks. To emphasize again, -the assembly names must be the GenBank accession identifier or -the UCSC database name, e.g.: 'GCF_016077325.2', or 'hg38', 'mm39'. -You can find a full list of all GenArk repository assemblies at: -assembly hub list +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 VEuPathDBGeneModels -shortLabel PAG 2026 contrib -longLabel PAG 2026 - demonstrating contributed tracks to UCSC GenArk assemblies -group genes -type bigBed 12 . -visibility pack -labelFields name +track myTrack +shortLabel My Track +longLabel My contributed annotation track for GenArk assemblies +type bigBed 9 + +visibility dense +bigDataUrl myTrack.bb searchIndex name -bigDataUrl veupathGenes.bb -colorByStrand 0,0,122 157,60,32 -dataVersion VEuPathDB release 68 -html ../documentation - -# can be multiple track definitions here for other annotations +html myTrackDocs+
-Since all the annotations are the same type, a single trackDb.txt -file is sufficient for all assemblies. The html link refers -to ../documenation.html as used in the hub.txt file. -For documentation structure, you can follow the typical UCSC track -format with sections for: Description, Methods, Credits, -References. For example: -typical UCSC track documentation. +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. +