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  Frequently Asked Questions: Linking to the Genome Browser
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  Linking to the Genome Browser from another software application
 

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

Response:
Link to the Genome Browser using a URL of the form:

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

  • 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 July 2003 human release, you would use db=hg16. 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
 

Question:
"How do I 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?"

Response:
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 hg18 human assembly at the position of the knownCanonical transcript associated with GABRA3:

http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg18&singleSearch=knownCanonical&position=GABRA3


  The hgsid parameter
 

Question:
"What is the hgsid parameter? Should I include it in URLs that link to the Genome Browser?"

Response:
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
 

Question:
"How can I create a custom URL to view only specific tracks in the Genome Browser?"

Response:
Each assembly in the Genome Browser has a set of default tracks that will display unless you specifically hide them in your URL. The easiest way to create your custom URL is by creating a session after logging into your account.

  • 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 something like the following:
    http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=User%20Name&hgS_otherUserSessionName=HideAllTracks
  • To display the tracks of your choice, simply add the table names to the end of the session URL in the format &[table name]=[display mode] (e.g. to add the Assembly track in full display mode, add "&gold=full" to the end of the URL).
  • If you don't know the table name for your track, in most cases, you can hover over either the gray bar at the left side of the Browser's graphical display or the track name in the track listing below the Browser's graphical display. A URL will be displayed at the bottom left corner of your screen and the table name will be at the end of that URL in the format "g=[table name]".
  • A URL that displays the UCSC Genes track in pack mode and the RefSeq Genes in full mode would look something like the following:
    http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=User%20Name&hgS_otherUserSessionName=HideAllTracks&knownGene=pack&refGene=full