Video Tip of the Week: UCSC Track Hubs

Over the years we’ve seen some real shifts in the needs of the trainees in our UCSC Genome Browser workshops. At first, people just needed access to the reference genome and the data that was available (and boy, has that changed over the years–time travel back with this post!). But as researchers around the world had access to more and bigger data sets that they were generating themselves, they kept asking for ways to load up their own data into the browser framework to explore their data with more context and with existing tools like the Table Browser for more queries.

We relayed this back to the UCSC team, and we know they were hearing it from other sources too. And besides the initial basic custom tracks that had been available, more ways to load up bigger data sets (the big-formats) and related tracks (super-tracks) became options. The biggest change, though, came with the Track Hubs. Now you aren’t just loading up a couple of tracks–you can load up complex collections with the hub framework. Check out the existing ones by going to the track hubs button from the Gateway:

Locate the hubs from the Gateway page.

Locate the hubs from the Gateway page.

You can use the public hubs to get a sense of what they can do–adding a lot of new info to a genome with new source data, new technologies, various special projects, etc. You can create your own Track Hubs to explore and query within existing assemblies. Or you can create entire new assemblies that UCSC doesn’t already host with Assembly Hubs. I touch on the basics of this in this week’s video tip.

But this was just a taste–click through to the documentation and wiki pages to learn more about the specifics of using these tools.

Hubs have been available for a little while and some early adopters have tried them out–like Pierre Lindenbaum did here–but they were the subject of much praise and chatter recently with the publication of a paper with more detail for people new to the hub functions. And a separate paper gave more detail on extending Assembly Hubs–that let you load up entirely new comparative genome data. You can create “snake tracks” that help you visualize comparisons, inversions, duplications, etc. And you don’t have to create a local mirror for these things.

Now, there may be some times where a local mirror is still your best bet. A lot of the places we talked to researchers were hospital research settings. If you have patient data that shouldn’t go outside of your firewall, for example, you may still want everything in-house. But for a lot of projects the Track Hubs can take care of the overhead for you instead.

You can use the hubs for your own work. Or if you have a collection of data that you want to offer to the wider community you can request that to the UCSC folks and possibly get that on to the public hubs page.

Check out the publications below for a grasp of the foundations–and also see the new directions that are being explored. Hubs are actually more flexible than just layering on new annotations, and you can read more about that too.

If you aren’t familiar with UCSC Genome Browser basics that you need to really understand the annotation tracks foundations, be sure to see the freely available materials that UCSC sponsors us to provide: Introduction and Advanced tutorials.

Quick links:

Track Data Hubs documentation: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

Assembly Hubs wiki page: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs

References:
Raney B.J., Dreszer T.R., Barber G.P., Clawson H., Fujita P.A., Wang T., Nguyen N., Paten B., Zweig A.S. & Karolchik D.  (2013). Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser, Bioinformatics, DOI:

Karolchik D., Barber G.P., Casper J., Clawson H., Cline M.S., Diekhans M., Dreszer T.R., Fujita P.A., Guruvadoo L. & Haeussler M.  (2013). The UCSC Genome Browser database: 2014 update, Nucleic Acids Research, DOI:

Nguyen N., Hickey G., Raney .BJ., Armstrong J., Clawson H., Zweig A., Kent J., Haussler D., Paten B. (2013). Comparative Assembly Hubs: Web Accessible Browsers for Comparative Genomics. arXiv:1311.1241v1 [q-bio.GN]