Interaction between UCSC and Galaxy

Importing Data from UCSC Table Browser to Galaxy

One of key features of Galaxy is its ability to obtain data directly from UCSC Table Browser. This can be done in one of the two ways:

  1. Directly from UCSC Table Browser
  2. Using Galaxy's UCSC Table Browser tool

This short screencast (stream) illustrates these two possibilities (requires QuickTime player).

When importing data from Table Browser to Galaxy it is advisable to set output format to BED as shown below (What is BED?):

http://www.bx.psu.edu/trac/local/TableBrowser.png

BED formatted data are most compatible with genomic interval operations.

Displaying Galaxy Data using UCSC Genome Browser

Any dataset in Galaxy's history can be displayed within UCSC Genome Browser as long as its chromosome, start, and end columns (so called metadata) are properly set and the corresponding genome assembly exists at the UCSC Browser.

Watch this screencast (stream) to see how to set metadata and display a Galaxy dataset at UCSC Genome Browser (requires QuickTime player).

Special thanks to Jim Kent and UCSC Genome Browser crew for making Galaxy connection to UCSC possible!