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 annotations, Custom -Tracks, Track Hubs, and Assembly Hubs. Note that the <input> format indicates a -user choice and not a valid example.
+Tracks, Track Hubs, and Assembly Hubs. In these examples, text in brackets "<" and ">" +indicate places where the user supplies information.You will be able to share Genome Browser sessions with the following link format:
http://genome.ucsc.edu/s/<userName>/<sessionName>
For instructions on creating a saved session, go to the session user guide. If you want to specify track settings in a URL directly, please read the section on setting track visibility via URL for a complete description.
Or if you prefer the older style, which allows you to link to different tools, you may use the following format:
-http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&gS_otherUserSessionName=<SessionName>
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&gS_otherUserSessionName=<sessionName>
This longer format has the flexibility of replacing "hgTracks" with different tool names 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. The following format will bring the recipient to a user's custom Table Browser selections:
-http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&hgS_otherUserSessionName=<SessionName>
http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&hgS_otherUserSessionName=<sessionName>
Both session link formats have the advantage of being able to add URL parameters to the end. The shorter link format requires a question mark before any URL parameters, with ampersand characters separating different parameters like so:
http://genome.ucsc.edu/s/view/clinicalzoom?textSize=18
The longer format requires an ampersand between each parameter, like so:
You can link to a specific genome assembly and position in the Genome Browser using a URL with
-the db= and position= parameters. Note that the <input>
-format indicates a user choice and not a valid example.
db= and position= parameters.
http://genome.ucsc.edu/cgi-bin/hgTracks?db=<assembly>&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
You can control the visibility of tracks from the URL with the following parameters, each linked by the "&" sign, similar to position parameters. For more information, please see the optional URL -parameters section of the Custom Tracks User's Guide. Note that the <input> format indicates -a user choice and not a valid example.
+parameters section of the Custom Tracks User's Guide.hideTracks=1 - hides all tracks<trackName>=hide|dense|pack|full - sets specified track or subtrack to a
chosen visibilitytextSize=<number> - sets browser text size to either 6,8,10,12,14,18,24,or
34. Default is a textSize of 8.ignoreCookie=1 - removes pre-existing user settings like track seletion, custom
tracks, and track hubsFor example, you can use the following command to hide every track (hideTracks=1) and set the knownGene track to the pack visibility (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.
<trackName>_hideKids=1 - hides a specific composite track's subtracks<trackName>_sel=1 - selects specific subtrack to be 'checked', allowing
displayFor 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+
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&position=chr21:34821279-34888690&hgct_customText=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb+
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr21:34821279-34888690&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.