The easiest way to save and share tracks from the URL is by logging in to your Genome Browser account and creating a saved session. -Saved sessions are a versatile way to share data that may include native data, Custom Tracks, and -Track Hubs.
+Saved sessions are a versatile way to share data that may include native annotations, Custom +Tracks, Track Hubs, and Assembly Hubs.-You will be able to save and share Genome Browser sessions with the following format: -
http://genome.ucsc.edu/s/userName/sessionName
-Or if you prefer a modifiable, longer URL; use this format:
-http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[UserName]&hgS_otherUserSessionName=[SessionName]
http://genome.ucsc.edu/s/userName/sessionName
For instructions on creating a saved session, go to the -Saved Session Help page.
-+session user guide. If you want to specify track settings in a URL directly, please read the section on -changing track visibility via URL for a complete description. -Note that these URL parameters do not work with the shorter session URLs. +setting track visibility via URL for a complete description. +Note that URL parameters do not work with the shorter session URLs.
+ ++Or if you prefer a modifiable, longer URL; use the following format:
+http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[UserName]&hgS_otherUserSessionName=[SessionName]
It has the advantage of being able to add additional URL parameters to the end and the +flexibility of replacing "hgTracks" with different tools to share saved settings on the Table +Browser (hgTables), Variant Annotation Integrator (hgVai), or Data Integrator (hgIntegrator). +This will preserve your option selections and can be useful to share.
You can link to a specific genome assembly and position in the Genome Browser using a URL with
the db= and position= parameters:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=[db]&position=[position]
Where:
db - designates a specific genome assembly. For example, db=hg19
refers to the Feb. 2009 human genome release. For a list of db parameter values that
correspond to UCSC assemblies, see the list of UCSC
releases.position - can be any search term 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
The hgsid is a temporary user ID that stores setting and custom track information in the URL. -Including it in any shared URLs is a privacy concern, and it should be removed when -constructing any links to the Genome Browser. Creating -Saved Sessions is the recommended way to -share Genome Browser information. -
- +http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000
You can control the visibility of tracks from the URL with the following parameters, -each linked by the "&" sign, similar to position commands. For the full list, please see the +each linked by the "&" sign, similar to position parameters. For the full list, please see the optional URL parameters section of the Custom Tracks User's Guide. Note that italic text indicates a user choice, not a working example.
-For example, you can use the following command to hide every track and set the knownGene track to -the pack visibility:
-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
Composite tracks have additional URL parameters that encode options to hide, select, and display subtracks.
For example, the following URL hides all tracks (&hideTracks=1), hides a specific composite track's default subtracks (&refSeqComposite_hideKids=1), turns on one specific subtrack (&ncbiRefSeqCurated=full), and checks a box to display that subtrack (&ncbiRefSeqCurated_sel=1).
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&refSeqComposite_hideKids=1&ncbiRefSeqCurated=full&ncbiRefSeqCurated_sel=1+ +
+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 example shows the hgct_customText parameter accepting
+a bigBed file URL as a custom track:
+
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb+ +
+If you want to add more information to the Custom Track, you can do so using the
+hgct_customText parameter. Since this is a URL, you must use "%20" to encode
+for spaces and "%0A" for a new line character. For example, the following example shows Custom
+Track input pasted in the custom track input box and the
+equivalent input in the URL:
+
+
browser position chr21:33038946-33039092 +track type=bam bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam name=Example description=ExampleBAM+
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=browser%20position%20chr21:33038946-33039092%0Atrack%20type=bam%20bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam%20name=Example%20description=ExampleBAM+
+More information on custom track parameters can be found in the +Custom Track user guide.
+ + + +Similar to custom tracks, track hubs can be loaded into the URL using the
+&hubUrl= parameter. This parameter takes input similar to the
+track hub input box. The following example
+links to the hg19 genome database and an example track Hub:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt+ +
Track hubs' track visibility can also be changed from the URL parameters. The following link +specifies the hg19 genome database (db=hg19), loads a track hub (hubUrl=http), hides all tracks +(hideTracks=1), hides the subtrack kids of a particular track (gtexRnaSignalMaleYoung_hideKids=1), +sets a specific subtrack to be displayed (gtexRnaSignalSRR1311243=full), and ignores user settings +(ignoreCookie=1).
+https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1>exRnaSignalMaleYoung_hideKids=1>exRnaSignalMaleYoung=full>exRnaSignalSRR1311243=full&ignoreCookie=1+ +
+To link to an assembly hub and display data on a non-natively supported genome, the same
+parameters apply. To specify the intended genome assembly, instead of using db=,
+you must use genome=araTha1, where araTha1 is the name set by
+your genomes.txt file in the line genome araTha1.
https://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt+
+To see the files behind that assembly hub, please visit the + +hub's directory. For more information on assembly hubs in general, please see the +assembly hub wiki, the track hub user guide, +or the quick start guide +to assembly hubs. + -
+
To jump directly to a gene's position on the Genome Browser, set the position parameter in the
URL to a gene symbol (e.g., TP53, MTOR, KRAS) and add the parameter
&singleSearch=knownCanonical. For example, the following link will open the
Genome Browser for the hg19 human assembly at the position of TP53 on the knownCanonical dataset
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. Instead of a position search,
gene descriptions use the &hgg_gene= URL parameter. The following URL connecting
to 'hgGene' will open up the Genome Browser description page containing protein function,
expression profile, and links to additional information for the gene TP53.
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, where
-"%20" is the URL encoding for spaces:
-Try the following example of the hgct_customText URL variable. -
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 using 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&db=hg19-
Hubs track visibility can also be changed from the URL parameters. The following link loads a -specific track from a supertrack with multiple composite subtracks.
-https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1>exRnaSignalMaleYoung_hideKids=1>exRnaSignalMaleYoung=full>exRnaSignalSRR1311243=full&ignoreCookie=1+ +
The hgsid is a temporary user ID that stores setting and custom track information in the URL. +Including it in any shared URLs is a privacy concern, and it should be removed when +constructing any links to the Genome Browser. Creating +Saved Sessions is the recommended way to +share Genome Browser information. +
+ ++For more information, please see our section +on URL parameters for custom tracks. If you cannot find what +you are looking for, please contact our active mailing list by emailing +genome@soe.ucsc.edu. All +messages sent to that address are publicly archived. If your question includes sensitive data, +you may send it instead to +genome-www@soe. +ucsc.edu