Contributed Tracks

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.

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:

• Develop your annotations in a track hub under your control.
• Provide a reference to your development track hub to the genome browser for inclusion consideration.
• By following the suggested outline, the browser will be able to efficiently add your annotations to the genome browser system.

Your track hub file/directory structure

+-- hub.txt
+-- genomes.txt
+-- documentation.html
+-- GCA_000260495.2/
|   +-- trackDb.txt
|   +-- veupathGenes.bb
|   +-- veupathGenes.gtf.gz
+-- GCF_014441545.1/
|   +-- trackDb.txt
|   +-- veupathGenes.gtf.gz
|   +-- veupathGenes.bb
+-- GCF_014108235.1/
|   +-- trackDb.txt
|   +-- veupathGenes.gtf.gz
|   +-- veupathGenes.bb

Requirements

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.

Example hub.txt file

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
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.

Example genomes.txt file

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

Example trackDb.txt file

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
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

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.