Tables in Track Hubs

[Shane Buckley]

Hello UCSC Genome Browser Team,

I am looking to use track hubs to extend a set of custom tracks that for a public session. I understand the bigBed file and how this is supplemented with an AutoSQL file.

Is it possible to set up a call/meeting to help us understand how to implement our specific requirements?

My questions are:

- is bigBed/AutoSQL in a track hub the correct approach?

- Is there a way to support hierarchical data?

- Is there a way to organize the AutoSQL fields as groups of tables?

We are essentially looking to add these mock-up tables to the on-click pop-up of our custom tracks:

Thanks in advance!

Best,

Shane Buckley

[Maximilian Haeussler]

Hi Shane,

we can't teach bioinformatics through calls, sorry, especially not for commercial companies. Email is OK.

My questions are:

- is bigBed/AutoSQL in a track hub the correct approach?

Yes. 

- Is there a way to support hierarchical data?

Yes and no, see below. 

- Is there a way to organize the AutoSQL fields as groups of tables?

Yes you can add JSON to the bigBed extra fields, see the trackDb statement extraTableFields. 

https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#extraTableFields

Let us know if this doesn't work. Also, note that the big AI tools all know a lot about our trackDb format and can probably make the trackDb file for you and also convert the BED files to bigBed.

best

Max