New viewing options in the UCSC Genome Browser

Last week there were a couple of announcements from the UCSC Browser team that I wanted to talk about. Both of them affect the visualizations you can do in the Browser.

New Drag and Reorder Functionality Released

....It is now possible to rearrange the order of tracks within the browser image.
To reorder tracks, click-and-hold the side label or gray mini-button of a single
track and drag the highlighted track to a new position within the image....

I’m going to do a quick movie of what that means–it has no audio just to keep it smaller and quick. But this will allow you to move the tracks you want closer together without going to the configuration page to do it now. It also means you may have to use the Default Tracks and Default Order buttons to go back to what the original views are. Keep that in mind if someone else shares a computer with you.

I want to mention a couple of glitches in this, though: some people have reported that in their stored sessions and custom tracks that the orders are being altered. And when you upload tracks now you don’t have the same configuration options, so you’ll notice that on your saved upload items.  Here’s a word from the team from the discussion mailing list:

We have noted your bug that some sessions that had tracks that were re-ordered using the old paradigm are now out of order. We are currently testing a fix and hope to have it out in a week or so.

New ENCODE Integrated Regulation track released

There are huge challenges in visualizing the wealth of ENCODE data that’s now coming out, and UCSC is actively developing new strategies and methods to manage the visualization needs. They have now added a new “super-track” to visualize some  of the data. I can’t link to this email as it is only for registered mailing list members, but here’s a piece of it. The whole thing is in the “News”  item on the UCSC home page right now http://genome.ucsc.edu/

The ENCODE Data Coordination Center at UCSC is pleased to announce the release
of the ENCODE Integrated Regulation super-track, a collection of regulatory
tracks containing state-of-the-art information about the mechanisms that turn
genes on and off at the transcription level.

Individual tracks within the set show enrichment of histone modifications
suggestive of enhancer and promoter activity, DNAse clusters indicating
open chromatin, regions of transcription factor binding, and transcription
levels. When viewed in combination, the complementary nature of the data
within these tracks has the potential to greatly facilitate our understanding
of regulatory DNA. (To view a browser session showing the ENCODE Integrated
Regulation super-track, see

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Example1&hgS_otherUserSessionName=hg18EncReg.

I know these came out last week, but I like to take a little while to explore the new features and get used to them before I speak to them–especially when they are significant alterations of the functionality. And it gives a bit of time to see if there are issues developing around the use of them.

We will update our training materials with these new features soon.  For the freely available materials sponsored by UCSC start here: http://www.openhelix.com/ucsc

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