Additional resources
Tracks accessed through a hub can be used in Genome Browser sessions and custom tracks in the same manner as other tracks. The data underlying data hub tracks can be viewed, manipulated, and downloaded using the UCSC Table Browser. To remove a track hub from your Genome Browser display, click the "Disconnect" button on the Track Hubs page.
For confidential or private data, please note that unlisted hubs are not secure. The URL helps to hide the location of the data; it is a simple barrier of obscurity. Please also know that hubs can be loaded from local directories when using GBiB.
-When sharing track hubs on a single assembly from manuscripts, publications, -or on research websites, we recommend using a session to link to -the Genome Browser view attached to that particular track hub. This has the advantage -of being able to save and share configuration settings made on other, native browser tracks. -The process for generating a session link to share a track hub for a manuscript is to -make the hub on your web-accessible server, attach the hub to the Genome Browser, configure +
When sharing track hubs on a single assembly, we recommend using +Saved Sessions +(for manuscripts, publications). These have the advantage +of being able to save and share configuration settings made on other browser tracks. +If you are just starting, an overview of the proces is to make the hub on +your web-accessible server, attach the hub to the Genome Browser, configure browser position and related tracks, then save your named session and share the session link. Your session links will be in the following format with your chosen username and session name:
--It is also possible to add or share a track hub directly by URL. If you add -hubUrl=[URL] to your hgTracks URL line, it will add the hub directly into the -browser:
+We have additional resources about Saved Session +sharing and, + +backup to a file.
++If you prefer URL manipulation, it is also possible to add or +share a track hub directly by URL +or otherwise modify the browser via URL. For example, if you add +hubUrl=[URL] to your hgTracks URL line, it will add the hub +directly into the browser:
If you are adding an assembly hub with multiple genomes, you can link directly to hgGateway, the assembly selection page and a particular genome:
-This section provides a step-by-step description of the process used to set up a track hub on your own server.
To create your own hub you will need:
See the searchIndex and searchTrix fields in the Hub Track
Database Definition document for
information on how to set up your bigBed to enable searching. The searchIndex setting requires
the input BED data to be case-senstive sorted (sort -k1,1 -k2,2n). You can use
either the example UNIX sort command or the bedSort utility available
here. See an example
searchable hub.
-Once you have successfully loaded your hub, by pasting the URL to the location of your hub.txt file -into the My Hubs tab of the Track Data Hubs -page, you may want to consider building URLs to directly load the hub along with session -settings.
--To build a URL that will load the hub directly, add "&hubUrl=" to the hgTracks -CGI followed by the address of the hub.txt file. You also need to include the UCSC assembly you -are displaying the hub upon such as "db=hg19". For example, here is a working link that -will visualize the ENCODE AWG hub: -
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt -If you also want to load your hub at specific browser coordinates and with a specific set of other -browser tracks (you can also set the visibility of each track in your hub), you can save your -hub in a session, which are in essence "View Settings" collected in a text file (example -session text files here). Sessions can be -shared in different ways, -please see the instructions for -creating a session and saving it to a file.
--By making your session file available over the Internet, you can build a URL that will load the -session automatically by adding "&hgS_loadUrlName=" to the hgTracks CGI followed by -the URL location of the saved session file. The location of the saved session file should be in the -same directory that holds your hub.txt file. Finally add "&hgS_doLoadUrl=submit" -to the URL to inform the browser to load the session.
--There are four required variables for your URL to load a session with a hub and an example URL:
-db - name of the assembly (e.g. hg19 or mm10)
-hubUrl - URL to your track hub
-hgS_loadUrlName - URL to your session file
-hgS_doLoadUrl - value should be "submit" http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://myLab.org/myHub.txt&hgS_loadUrlName=http://mySession&hgS_doLoadUrl=submit-
-Another feature one can use in place of "&hubUrl=" is
-"&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 http://university.edu/lab/folder/ directory (for example, hub1.txt, hub2.txt,
-ect.). This feature can be useful for dynamically generated hubs that might collect in the browser
-otherwise.
-Beyond the URL options of "&hubUrl=" and "&hubClear=" -there are many other ways to link to the Browser -including a list of URL optional parameters described in the the Custom Tracks User's Guide.
-If you would like to share your track hub with other Genome Browser users, you can register your hub with UCSC by contacting the Genome Browser technical support mailing list at genome@soe.ucsc.edu. Please include the URL of your hub.txt file in the message. Once registered, your hub will appear as a link on the Public Hubs tab on the Track Hubs page. To assist developers of Public Hubs, there is a Public Hubs Guidelines page. The page shares pointers and preferred style approaches, such as the need for creating description html pages for your data that display any available references and an email contact for further data questions.
Alternatively, you can share your track hub with selected colleagues by providing them with the URL