- Genome Browser
- My Data
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. In these examples, text in brackets "<" and ">" indicate places where the user supplies information. Note that the brackets are not needed for the URL, including the brackets will result in a 'Could not find session' error.
You will be able to share Genome Browser sessions with the following link format:
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:
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:
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:
Both formats require an ampersand between each additional parameter, seen in the longer format like so:
You can link to a specific genome assembly and position in the Genome Browser using a URL with
db- designates a specific genome assembly. For example,
db=hg19refers 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
The following link is an example of a URL that declares assembly and position:
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.
hideTracks=1- hides all tracks
<trackName>=hide|dense|pack|full- sets specified track or subtrack to a chosen visibility
textSize=<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 hubs
For example, you can use the following command to hide every track (hideTracks=1) and set the knownGene track to the pack visibility (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 display
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).
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:
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
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:
Track hubs' track visibility can also be changed from the URL parameters. The following link specifies the genome database (db=hg19), loads a track hub (hubUrl=http.../hub.txt), 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).
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
you must use
genome=araTha1, where araTha1 is the assembly name set by
your genomes.txt file in the line
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
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.
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 email@example.com. 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