For additional information, see sharing Saved Sessions and backing up custom data.
--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:
+ + + + + +Hubs can be loaded into the URL using the hubUrl= parameter. This parameter
+takes input similar to the track hub input box.
+Native UCSC supported genomes can be loaded into the URL using the db= parameter while
+non-natively supported genomes such as assembly hubs or genArk hubs use the genome=
+parameter. URL parameters can be combined by using &.
+
The following example links to the hg19 genome database and an example track hub using the db= and the hubUrl= parameters:
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. As an example, the +following link specifies:
+https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1>exRnaSignalMaleYoung_hideKids=1>exRnaSignalMaleYoung=full>exRnaSignalSRR1311243=full&ignoreCookie=1+ + + +
guidelines=on/off - activate or deactivate the blue guidelineshgFind.matches=<listOfNames> - highlight features given their nameshgt.reset=1 - show only the default trackshgt.toggleRevCmplDisp=1 - show the reverse-complementhgt.labelWidth=<number> - set the size of the left-side label areahideTracks=1 - hide all trackshideTracks=1&<trackName>=full|dense|pack|hide - hide all tracks and show
+other trackshighlight=<db>.<chrom>:<chromStart>-<chromEnd>#<color>|...ignoreCookie=1 - do not load the user's existing settings saved
+in the internet browser's UCSC Genome Browser cookie. This means that the link will show the
+Genome Browser default settings such as track selections, custom tracks, and track hubs. Any
+changes you make in this new session will, however, affect the user's settings. E.g., if you add a
+track in this new window, and come back to the genome browser later, the track will still be there.
+This setting is useful if a website wants to link to the Genome Browser, starting with a "clean
+slate" but believes the user will come back to the Genome Browser expecting the changes to still be
+there.ruler=hide - hide the ruler at the top of the browser imageoligoMatch=pack&hgt.oligoMatch=<dnaSeq> - switch on the Short Match track and
+highlight a matching sequencepix=<number> - set the width of the image in pixelstextSize=<number> - set the size of text font<trackName>=full|pack|dense|hide - show your current tracks, adding a track
+and set it to full, pack or dense visibility or hide it<trackName>_imgOrd=<number> - vertically orders the tracks on the image
+based on the numbers provided. You need to specify an order for every visible track when using this
+parameter<trackName>.heightPer=<number> - sets the height of the a bigWig track
+in pixels<trackName>_hideKids=1 - hides a specific super track's individual tracks<trackName>_sel=1 - selects specific subtrack to be 'checked', allowing
+display-If you are adding an assembly hub with multiple genomes, you can link directly to hgGateway, -the assembly selection page and a particular genome:
+You can create a URL with multiple Track Hubs using thehubUrl= parameter. URL
+parameters can be combined by using &. For example, using the following track hubs:
+
++ENCODE DNA Trackhub +https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/hub.txt ++
+JASPAR TFBS +http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt ++
+ReMap 2022 Regulatory Atlas +https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt ++
+The combination of the three hubs allows the creation of the following URL that can load the +three hubs on the Genome Browser. +
++https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/hub.txt&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&hubUrl=https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt+ +
+The following example links to an assembly hub using the hubUrl= and
+genome= parameters where in the example, genome=araTha1, is the assembly
+name set for genome in the genomes.txt file. URL parameters can be combined by using &.
https://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt+ +
hubClear=connects the hub and disconnects other hubs that are in the same directoryhgHubConnectReplacing hgTracks with this parameter connects the hub and redirects the link to the
+Track Data Hubs pagehgHubConnect.remakeTrackHub=on
+acts to connect when pointed to /hgHubConnecthgHub_do_firstDb=1
+uses the first database in genomes.txthgHub_do_redirect=on
+redirects the attached hub to the Gateway page
+The following example link connects the hub and redirects the link to the Gateway page to display
+the hub's description html page, which is defined in the genomes.txt by the htmlPath
+setting, by using hgHubConnect, hgHub_do_redirect=on,
+hgHubConnect.remakeTrackHub=on, hgHub_do_firstDb=1, and
+hubUrl.
+
+
http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt
+
+You can also link to the Gateway page to display the hub's description html page by using the
+hgGateway and genome parameters. The following example links the hub to
+the Gateway page:
http://genome.ucsc.edu/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt
+You can create a URL for an assembly hub with track hubs using a combination of the
+hubUrl= and genome= URL parameters. URL parameters can be combined by
+using &.For example, using the following assembly hub and track hubs:
+
+Arabidopsis thaliana assembly hub +https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubPlants/cshl2013/hub.txt ++
+ReMap 2022 Regulatory Atlas +https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt ++
+UniBind 2021 Robust hub +https://unibind.uio.no/static/data/latest/UniBind_hubs_Robust/UCSC/hub.txt ++
+The combination of the three hubs, along with genome=araTha1, allows for the creation of
+the following URL that can load the three hubs on the Genome Browser.
+
+https://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubPlants/cshl2013/hub.txt&hubUrl=https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt&hubUrl=https://unibind.uio.no/static/data/latest/UniBind_hubs_Robust/UCSC/hub.txt+ + + +
+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)
+GenArk assembly.
+
+To create a link to the track hub that references a GenArk assembly, the
+genome=GCA_002844635.1 and hubUrl= URL parameters can be used like in the
+following example:
+
+https://genome.ucsc.edu/cgi-bin/hgTracks?genome=GCA_002844635.1&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGenArkExample/genArkTrackHub/hub.txt ++
This section provides a step-by-step description of the process used to set up a track hub on your own server. If you would like information about how to attach a track hub to an existing assembly hub, please refer to the following FAQ entry.
To create your own hub you will need: