GNomEx now serves as a repository for files visualized in the following genome browsers:

• IGB
• IGV
• UCSC Genome Browser.

GNomEx Raw experiment files -> GNomEx Analysis files -> GNomEx Data Track files -> Genome Browsers

In order to create Data Tracks to distribute for visualization, an Analysis must first be created. Then the specific files supported by the browser (e.g., bam, useq, etc.) can then be dragged to the Data Track file.

How to Navigate to a Data Track

The Data Tracks view is organized by Organism and Genome Build. The view supports a nested folder structure so that like data tracks can be grouped together. You can look up a Data Track by data track number. The data tracks have the number 'DTxxx'.

Properties are ported over to the GNomEx model, so you will be able to define properties using 'Configure Properties' from the GNomEx home page.

How to Create a Data Track

To perform the link, create or click on an existing Analysis and go to the files tab. Click on the 'Distribute Data Tracks' link.

The Distribute Data Tracks window will appear and filter based on the Organism, Genome Build, and Lab group. You may need to deselect the lab group from the dropdown if you want to see all data tracks for this genome build.

Select an analysis file and drag-and-drop it to the data track tree. If you drag it onto an existing data track, it will link the analysis file to that data track. If you drag it over a folder or genome build folder, it will create a new data track, giving it the name of the analysis file.

The Data Tracks window will continue to stay visible after you have linked/created a data track. You can click on another analysis file or another analysis and perform the same operation again.

The Analysis Detail view has a Data Tracks tab that will show you links to all of the data tracks. Click on the link to go to the Data Tracks view.

On the Files tab of the Data Track Detail view, the analysis number that the data track file is link appears in the files grid.

When you remove an Analysis or an Analysis file that is linked to data track(s) you will get a message that the data tracks must be unlinked or removed first. Let me know if you would like to happen automatically.

Remember to click the 'Refresh DAS/2 server' when you are ready to distribute the data tracks to the DAS/2 server.

How to visualize the Data Track in a Genome Browser

Data Tracks can be visualized in three genome browsers: IGB, IGV, and the UCSC Genome Browser. To launch IGV or the UCSC Genome Browser, click on the link in the top right corner. (The link will be disabled if the file type is not supported by the browser.)

To launch IGB, click on one of the links that will launch Webstart for IGB. Now you are ready to connect to this data source in IGB. http://myserver.somewhere.edu:8080/das2gnomex/genome. Set up a data source with this URL. The server you want may already be preconfigured. Look for the URL in the available servers and select it if present.

To load DataTracks from within IGV, first create an IGV server within GNomEx by clicking the IGV Browser button after selecting any DataTrack. Copy the URL in the popup.

Launch IGV and replace the Data Registry URL with this link (View -> Preferences -> Advanced).

Select tracks to load from within IGV (File -> Load from Server -> click checkbox to expand last server)

If you wish, use the URL Links button to fetch a URL to the file. This can be pasted into a variety of applications that can Load From URL (IGB, IGV, GBrowse, UCSC).

Lastly, clicking the UCSC Browser button after selecting a DataTrack will open a new window and load the UCSC Browser and your DataTrack as custom tracks. Repeat to add additional tracks. Which UCSC Browser is loaded can be configured in the MyAccount page.