- 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 parameters:
Here is an example:
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:
Another option for sessions is to download the file and host it in an external location and load it with
hgS_loadUrlName=<URL> allowing you to externally maintain your session,
or update it as you wish. Here is an example:
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,
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
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 link directly to the default position of an assembly by passing the
position=default parameter. This can be helpful in cases where
a track exists on multiple assemblies, and you want to build links to each of them. If no
position variable is passed, the Genome Browser assumes the default position for the
default assembly (hg38).
Here is an example which opens the uniprot track at the default position for sacCer3:
To link to a specific HGVS identifier, you can construct a link with the HGVS identifier
in the position field instead of coordinates. The default padding is 5bp on either side,
but you can always zoom in or out with
The numbers 1 through 4 zoom in or out corresponding to the buttons above the track window.
The following lists the zoom levels of each number, applicable to zooming in or out:
hgt.out1=submit zooms out 1.5x
hgt.out2=submit zooms out 3x
hgt.out3=submit zooms out 10x
hgt.out4=submit zooms out 100x
The following link is an example which leads to the variant NM_00257:c.1208G>T and zooms out 3x:
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
textSize=<number> - sets browser text size to either 6, 8, 10, 12, 14, 18,
24, or 34. Default is a textSize of 12.
<trackName>.heightPer=<###> - sets a bigWig track's height to a
particular number of pixels (between 20-100)
ignoreCookie=1 - removes pre-existing user settings like track selection, custom
tracks, and track hubs
For example, you can use the following command to hide every track (hideTracks=1), set the genome database to hg38 (db=hg38), set the mappability track to full visibility (mappability=full), and set the umap track height to 100 pixels (umap24Quantitative.heightPer=100). Each of these parameters can be used individually or in combination.
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
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).
If you have a custom track on a web-accessible server, you can use the location of the file
to load it directly as part of a URL.
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.
hubClear= to remove hubs at the same location
Another feature one can use in place of
hubClear=, which will load a hub while simultaneously disconnecting
or clearing, hubs located at the same location. For example, adding
hubClear=http://university.edu/lab/folder/hub10.txt would connect the
referenced hub10.txt while simultaneously disconnecting any hubs that might be
displayed from the same
(for example, hub1.txt, hub2.txt, etc.). This feature can be useful for dynamically
generated hubs that might collect in the browser otherwise.
hubClear there are other parameters
you can add to either if you wished, for instance, to attach an assembly hub and
display the Gateway page, while also sharing your contact email.
acts to connect when pointed to /hgHubConnect
uses the first database in genomes.txt
redirects the attached hub to the Gateway page
By pointing the URL to
/cgi-bin/hgHubConnect the hub would be connected to
and then redirect to the Gateway page to display the page in
htmlPath ../newOrg.html line. Here is an example:
genome= for assembly hubs
There is also another way to connect an assembly hub using the
genome= to arrive at
the Gateway page if you know the genome in
genomes.txt that you wish to display.
For instance, the below link skips the redirection step, where your
hub.txt contact email gets displayed, by pointing to the
It is possible to attach a track hub to an assembly hub via the URL using a combination of the
genome= URL parameters. For example, using the following
assembly hub and track hub:
Arabidopsis thaliana assembly hub https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubPlants/cshl2013/hub.txt
ReMap2020 Reg. Atlas track hub https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubRemap/remap.txt
The combination of the two hubs, along with
genome=araTha1, allows for the creation of
the following URL that can load both hubs on the Genome Browser.
When creating a track hub for a GenArk assembly, there is no need to do any attaching of the
assembly hub itself via the
hubUrl= URL parameter. GenArk hubs will automatically
attach themselves if the track hub mentions the GCA_ or GCF_ name identifier of the assembly hub.
Simply load the track hub on the Genome Browser, and the assembly hub will automatically appear. For
example, the following example track hub will load an additional track for the pig (GCA_002844635.1)
To create a link to the track hub that references a GenArk assembly, the
hubUrl= URL parameters can be used like in the
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. Most significantly, it will change after you share it. Anyone using it will see that last thing you did, not what you thought you were sharing. 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 firstname.lastname@example.org. 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
Visit our YouTube channel.
Visit our YouTube channel.
Visit our YouTube channel.