Tuesday, March 18, 2014

Using UCSC Genome Browser Sessions to Organize and View MethBase Tracks

I would like to share a tip that uses the UCSC Genome Browser Sessions to organize and view MethBase tracks.

As of 03/18/2014, MethBase contains 2294 tracks, including tracks for methylation levels, read depths, HMRs, etc. For human alone, there are 1130 tracks. Since each one may be interested in different set of samples and different selection of features, and want to display them with specific settings, there is no single setting that satisfies everyone. Fortunately, the UCSC Genome Browser Sessions provides a nice feature for you to 1) manually tailor a set of tracks (e.g., brain related), 2) store them for future re-use, and 3) share them with others. With UCSC Genome Browser, each one will have a "personalized" view of MethBase.

Using the Session feature requires you to create an account with UCSC Genome Browser and is quite straightforward (http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html). For example, here is a UCSC browser session that contains high coverage methylomes of normal cell samples from human (link).

Hopefully, more interesting and useful sessions, such as brain development oriented and cancer oriented, will be created and shared.