-See also:
-+The easiest way to save and share tracks via URL is by +logging in to your Genome Browser account and +creating a saved session. +Saved sessions are a versatile way to share data and may include native data, Custom Tracks, and +Track Hubs.
++You will be able to save and restore Genome Browser sessions with the following formats: +
http://genome.ucsc.edu/s/userName/sessionName+
+Or if you prefer the modifiable, longer format URL, use this format:
+http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[UserName]&hgS_otherUserSessionName=[SessionName]+
+For instructions on creating a saved session, go to the +Saved Session Help page.
++If you want to specify track settings in a URL directly, you can do so by naming the track and +visibility option directly in the URL. Note that these track parameters do not work on the shorter +session URLs. For example, the following URL parameters displays the hg38 genome database with the +Known Gene track in pack mode and the RefSeq Genes in full mode: +
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&knownGene=pack&refGene=full
-You can make a link to a specific position in Genome Browser using a URL with the db=
+You can link to a specific position in the Genome Browser using a URL with the db=
and position= parameters:
../cgi-bin/hgTracks?db=[db]&position=[position]http://genome.ucsc.edu/cgi-bin/hgTracks?db=[db]&position=[position]
Where:
db=hg19. For a list of the db parameter values that
+ db - designates a specific genome assembly. For example, db=hg19
+ refers to the Feb. 2009 human genome release. For a list of the db parameter values that
correspond to UCSC assemblies, see the list of UCSC
releases.position=chr1:35000-40000.position - can be any search value valid for the genome specified, including
+ a position range or a gene identifier. This often takes the form of
+ position=chr1:35000-40000.The following link is an example of a URL that declares assembly and position:
-http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000- - -
-Set the position parameter in the URL 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?db=hg19&singleSearch=knownCanonical&position=GABRA3
-The following URL connecting to 'hgGene' will open up the Genome Browser description page
-containing descriptions, expression, and links to associated information for the above gene.
-Note the use of the URL parameter hgg_gene=:
http://genome.ucsc.edu/cgi-bin/hgGene?db=hg19&hgg_gene=GABRA3 http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000
-The hgsid parameter is a temporary, internally used parameter that stores information -about what tracks the user last viewed, what position they were at, and what display settings they -had enabled. This should not be used when constructing links to the Genome Browser and could -unintentionally give someone access to private user data.
+hgsid=724184099_ZY6sql8XPIZcZx9b2RJm2aQBBZ78
-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:
-http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[User Name]&hgS_otherUserSessionName=[Session Name]http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[User Name]&hgS_otherUserSessionName=[Session Name]&gold=full -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 The hgsid is a temporary user ID that stores display setting and custom track information. +Including it in any shared URLs is a privacy concern, and should be removed when +constructing any links to the Genome Browser. Creating +Saved Sessions is a much safer way to +share particular Genome Browser views. +
-You can control the visibility of tracks via the URL with the following parameters, each linked by the & sign, similar to previous commands. Here are a few commands you can use -to control track visibility. Note that bold text indicates a variable and not -actually an example.
+to control track visibility. Note that italic text indicates a user variable and not +a valid a option.For example, you can use the following command to only show the knownGene track:
-http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack+
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack
You can use the following command to go to a particular position:
-http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:11000-20000+
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:25000-30000
You can use the following command to go to a particular gene:
-http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=KRAS&singleSearch=knownCanonical+
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=KRAS&singleSearch=knownCanonical+
URL optional +parameters section of the Custom Tracks User's Guide.
+ + + +
+To jump directly to a gene's position on the Genome Browser, set the position parameter in the
+URL to a gene symbol (TP53, MTOR, KRAS, etc.) 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 TP53:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position=TP53
+
+You can also link directly to gene description pages from the URL. The following URL
+connecting to 'hgGene' will open up the Genome Browser description page
+containing funtion information, expression profile, and links to associated information for the above gene.
+Note the use of the URL parameter hgg_gene=:
http://genome.ucsc.edu/cgi-bin/hgGene?db=hg19&hgg_gene=TP53
You can combine the URL visibility settings with the hgct_customText= parameter using
a track line you would otherwise put in the custom track
input box. The following is an example of the hgct_customText URL variable:
Try the following example of the hgct_customText URL variable, note that the hub only has data on chromosome 21:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigBed%20bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb
Similar to Custom Tracks, track hubs can be loaded into the URL usig the hubUrl=
parameter. This parameter takes input similar to the Track Hub interface. Try the
following example for reference:
http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt&genome=hg19