Re-creating UCSC's public gene tracks with custom data

[Katie Kyle]

Hello, 

Is it possible to re-create the gene tracks (Gencode/RefSeq/UCSC) such as the ones available for human and mouse with custom data on a mirror? Specifically, I am interested in being able to select different gene labels to display, the ability to search on the different gene IDs and even associated annotation text, and making the customized gene track description pages. 

From what I've found looking through help online and peeking through the public MySQL databases, these tracks seem to be genePred type. However, the genePred track we have created has more limited utility compared to the ones for human, mouse, and others at genome.ucsc.edu. 

Any help would be very appreciated!

Best, 

Kat

[Matthew Speir]

Hi Katie,

Thank you for your question about gene tracks in the UCSC Genome Browser.

Unfortunately, it would be quite difficult to integrate your gene data with the existing gene details pages for the UCSC Genes, GENCODE Genes or RefSeq Genes tracks as they are dependent on a number of difficult to recreate tables. Additionally, many of these table names and dependencies are hard-coded into the code that generates these details pages, making it difficult to adapt them to new data.

However, you can create bigGenePred files and add extra fields to these files to create robust item details pages for gene tracks on your mirror. The bigGenePred format page, https://genome.ucsc.edu/goldenPath/help/bigGenePred.html, contains a lot of great information on creating your own files. Note that while there is a sample AutoSql (.as) file linked on the page, it only includes the standard fields. You can add extra fields to this .as file that contain whatever information you want. Once you've created your bigGenePred files, you can then create a trackDb statement for them and load them into your mirror like you would other tracks you've loaded into your mirror.

An example of such a track that uses extra fields on a bigBed file (closely related to bigGenePred) to create a comprehensive item details page is our "ClinVar Main" track: https://genome.ucsc.edu/cgi-bin/hgc?db=hg38&c=chr1&l=11102836&r=11267747&o=11122121&t=11122122&g=clinvarMain&i=C%3EA.

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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