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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:

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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:

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:

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