We have been working with the folks for years to provide training on the UCSC Genome Browser*. And we’ve seen many changes in this time. But of course the biggest change has been in the sheer volume of data over there. It’s hard to know what’s even available because there’s so much. We used to show people this list of the tables (called the annotation database), but in one of the upgrades that was no longer getting updated. We missed it a lot.
When we do our workshops (which are about 3 hours long) we do an intro piece and a more advanced piece that covers the Table Browser. In neither one do we have the time to cover all of the data types that appear in the tracks. In the intro we show an overview of the whole page, and we mention that to learn about the tracks you need to click the menu names over there–but they can be obscure abbreviations, and it’s a little bit of hunting/pecking. A quicker way to scan them all with a bit more descriptive text is to click the “Configure tracks and display” buttons to see a list of all the tracks in a species in one list. That doesn’t have all the related tracks, but it’s at least a better summary of the options.
In our Table Browser tutorial we highlight the “describe table schema” button that gives you a sense of what a table contains at a more granular level, and gives you a list of linked/related tables. But that requires you to have already chosen a table.
So the HOT HOT HOT news today: there’s a track search feature that’s been announced. It’s going to make finding the data you are interested in MUCH easier to find now. The full announcement will be pasted below when it arrives. Be sure to check it out!
Where to find it–you can use the button on the Gateway search page:
I’ve been testing it a little bit and I think it will be a huge help. I used things like “rna-seq” to pull up tracks that have that data, and it looked right to me. I tried “antibody” to see what it got in the Yale Transcription Factor Binding Sites (TFBS) data set that everyone asks me about. And I specifically tried a couple of TFBS types (NFKB and Stat1) and was able to find tracks that contain those specifically. I think the results might be a little confusing for those if you didn’t know quite how to use them (but I specifically cover that track in the new ENCODE tutorial sponsored by the UCSC ENCODE team). You may have to go in and turn on the specific cell type + detection antibody data track on the details page.
Yay UCSC! Thanks so much for this. We’ll definitely be using it, and talking it up. I’m updating my slides this week and they will include this feature. I will ask them to also put it on the Table Browser page, though–I think it would be handy to have there as well.
The announcement mailing list item should arrive soon–I just noticed the button as I reloaded my browser just now….
EDIT 2: and here’s the official announcement now:
*UCSC sponsors the OpenHelix tutorials so that they are free to everyone.