Frequently Asked Questions: Linking to the Genome Browser

Topics

• Linking to the Genome Browser from another software application
• Linking to the browser at the position of a knownCanonical transcript associated with a gene symbol
• The hgsid parameter
• Creating a custom URL to view specific tracks

See also:

• The URL optional parameters section of the Custom Tracks User's Guide.

• The Customizing direct links section of the UCSC Genome Browser wiki page.

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Linking to the Genome Browser from another software application

How do I construct a hyperlink to the Genome Browser from my software?

Make a link to the Genome Browser using a URL of the form:

http://genome.ucsc.edu/cgi-bin/hgTracks?org=[org]&db=[db]&position=[position]

Where:

• org - specifies the genome in which you're interested (see Displaying Your Own Annotation in the Genome Browser for a list of acceptable values). This parameter defaults to the latest Genome Browser assembly for that species.
• db - designates a specific assembly version. For example, to refer to the Feb. 2009 human release, you would use db=hg19. The db parameter takes precedence over the org parameter. For a list of the db parameter values that correspond to UCSC assemblies, see the list of UCSC releases.
• position - can be any search value valid for the genome specified by org.

Linking to the browser at the position of a knownCanonical transcript associated with a gene symbol

How do I make a link to the browser from my application so that it will open at the position of the transcript in knownCanonical table that is associated with a given gene symbol?

Using the URL described above, set the position parameter to the gene symbol and add the parameter singleSearch=knownCanonical. For example, this link will open the Genome Browser for the hg19 human assembly at the position of the knownCanonical transcript associated with GABRA3:

http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg19&singleSearch=knownCanonical&position=GABRA3 

The following URL will open up the Genome Browser description page containing links to associated information for the above gene:

http://genome.ucsc.edu/cgi-bin/hgGene?org=human&db=hg19&hgg_gene=GABRA3 

The hgsid parameter

What is the hgsid parameter? Should I include it in URLs when I make a link to the Genome Browser?

The hgsid parameter is a temporary, internally used parameter that should not be used when constructing links to the Genome Browser.

Creating a custom URL to view specific tracks

How can I create a custom URL to view a specific subset of tracks in the Genome Browser?

Each assembly in the Genome Browser will display using a default set of tracks unless you specifically modify the track set in your URL. The easiest way to construct your custom URL is by logging in to your Genome Browser account and creating a session:

• Browse to the assembly of your choice (e.g. hg19).
• Click the "hide all" button. All tracks should now be hidden.
• Click the "My Data" pulldown in the blue navigation bar at the top of the screen to access Sessions.
• In the "Save Settings" section under "Save current settings as named session:", enter a name for your session.
• Check "allow this session to be loaded by others" if you want others to be able to access your session and URL.
• Click the "submit" button.
• Click the "Browser" link under "My Sessions" to open your session in the Browser. Your session URL should look similar to this:

  http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[User Name]&hgS_otherUserSessionName=[Session Name]

• To display the tracks of your choice, simply add the names of the tables associated with the tracks to the end of the session URL in the format "&[table name]=[display mode]". For example, to add the Assembly track in full display mode, add the table name "&gold=full" to the end of the URL:

  http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[User Name]&hgS_otherUserSessionName=[Session Name]&gold=full 

  If you don't know the table name for a track, in most cases you can view it by hovering the mouse cursor over either the gray bar to the left of the Browser's graphical display or the track's name in the group listings below the graphical display. In these cases the Browser will display a URL in the bottom left corner of the window, ending with the table name in the format "g=[table name]".

Here is an example of a URL that displays the UCSC Genes track in pack mode and the RefSeq Genes in full mode:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[User Name]&hgS_otherUserSessionName=[Session Name]&knownGene=pack&refGene=full