New navigation feature in UCSC Genome Browser

The new options just keep coming! It continues to get easier and easier to use the UCSC Genome Browser.

We’ve been working with UCSC to deliver training materials and workshops since 2003 and every training we do yields feedback about features that users would like to have. And it is very cool to see modifications and improvements come along. In the last year or so it seems they’ve been coming along so quickly that I have to update my slides about once a month!

This new feature provides one-click access to a number of the navigation features that it usually takes me a entire (and complicated) slide series to cover. Here is a screen shot of the menu options on a human genome region. You can right-click (with a PC) or control-click (with a Mac) to yield this popup dialog box that lets you get DNA, get an image, or get details about the items you click.  The choices vary a bit by track, of course. And I can’t seem to get SNP details when I click on SNPs. Also, as these are new, you might see some changes and fixes.

You can read the full announcement on the mailing list, and it currently also appears on the UCSC Genome Browser main page.You may need to allow popups from UCSC, and have a javascript configuration option set properly to enable everything.

[Genome-announce] New! Genome Browser right-click navigation

In the latest update of the UCSC Genome Browser, we’ve introduced a new right-click navigation feature. Several of the common display and navigation operations offered on the Genome Browser tracks page may now be quickly accessed by right-clicking on a feature on the tracks image and selecting an option from the displayed menu. Depending on context, the right-click feature will let you change the track display mode, zoom in or out to the exact position coordinates of the feature, open the “Get DNA” window at the feature’s coordinates, display details about the feature, open a popup window to configure the track’s display, or display the entire tracks image in a separate window for inclusion in spreadsheets or other documents. (Note that the “PDF/PS” option in the Genome Browser top navigation bar can also be used to generate a high-quality annotation tracks image suitable for printing.) ….[more at the link]

Anyway–try it out! It should make working with the browser easier than ever. And I’ll be updating my slides soon and they’ll be available for download.  The folks at USC will be the first to see those new slides live in the upcoming workshop there (and thank you very much for inviting us to southern California in mid-winter!!)

UPDATE: Larry Meyer (one of the developers of this feature) spotted my issue with the SNPs. Turns out you have to not have the view set to “dense” mode. Even though I was zoomed way in on a single SNP, unless you are in one of the other modes you can’t get to the details page. But if you are in–say Pack–it works fine to get SNP details.

Thanks Larry!

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