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Data Visualization

IGV is the recommended browser for exome data. The individual alignment and variation files can be downloaded from GnomEx and loaded into IGV by navigating to the File menu and selecting Load From File. Users can also stream the data directly from GNomEx after setting up a personal data repository. Steps to set up a personal repository:

  1. Log into GNomEx
  2. Click on the Data Tracks button at the top of the page.
  3. Select any datatrack file from the left navigation panel. Datatrack files have a blue icon next to them are often contained in directories.
  4. When a datatrack is selected, an information panel should appear to the right of the navagation panel. A button labeled IGV Browser should be located at the top of the information panel. Click on this button and select OK, if prompted.
  5. It takes a few seconds to a minute to create your repository. When it finishes, a message box is displayed with a link at the bottom. Copy this link.
  6. Open IGV
  7. Click on the View menu and select Preferences. Click on the Advanced tab. Click on the Edit Server Properties checkbox and replace the Data Registry URL text with what you copied. Click the OK button.
  8. Click on the File menu and select Load from Server. Navigate to your uNID and select the files you want to stream.

The repository only needs to be set up once. After it is setup, you can simply go the the File menu and select Load from Server. If new files are added to the demo or if you create new datatracks in other projects, you'll need to re-click the IGV Browser button, but don't have to copy and paste the URL into IGV. Please contact the Bioinformics Shared Resources with questions about visualization.