-The easiest way to save and share tracks via URL is by +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 and may include native data, Custom Tracks, and +Saved sessions are a versatile way to share data that may include native data, Custom Tracks, and Track Hubs.
-You will be able to save and restore Genome Browser sessions with the following formats: -
http://genome.ucsc.edu/s/userName/sessionName+You will be able to save and share Genome Browser sessions with the following format: +
http://genome.ucsc.edu/s/userName/sessionName
-Or if you prefer the modifiable, longer format URL, use this format:
-http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[UserName]&hgS_otherUserSessionName=[SessionName]+Or if you prefer the a modifiable, longer URL; use this format: +
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[UserName]&hgS_otherUserSessionName=[SessionName]
For instructions on creating a saved session, go to the Saved Session Help page.
-If you want to specify track settings in a URL directly, you can do so by naming the track and -visibility option directly in the URL. Note that these track parameters do not work on the shorter -session URLs. For example, the following URL parameters displays the hg38 genome database with the -Known Gene track in pack mode and the RefSeq Genes in full mode: -
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&knownGene=pack&refGene=full
-You can link to a specific position in the Genome Browser using a URL with the db=
-and position= parameters:
db= and position= parameters:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=[db]&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 the db parameter values that
+ 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 value valid for the genome specified, including
+ position - can be any seach 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
hgsid=724184099_ZY6sql8XPIZcZx9b2RJm2aQBBZ78
The hgsid is a temporary user ID that stores display setting and custom track information. -Including it in any shared URLs is a privacy concern, and should be removed when +
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 a much safer way to -share particular Genome Browser views. +Saved Sessions is the recommended way to +share Genome Browser information.
+-You can control the visibility of tracks via the URL with the following parameters, -each linked by the & sign, similar to previous commands. Here are a few commands you can use -to control track visibility. Note that italic text indicates a user variable and not -a valid a option.
+You can control the visibility of tracks from the URL with the following parameters, +each linked by the "&" sign, similar to position commands. For the full list, please see the +optional URL +parameters section of the Custom Tracks User's Guide. Note that italic text indicates +a user choice, not a working example.-For example, you can use the following command to only show the knownGene track:
-http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack-
You can use the following command to go to a particular position:
-http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:25000-30000-
You can use the following command to go to a particular gene:
-http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=KRAS&singleSearch=knownCanonical-
URL optional -parameters section of the Custom Tracks User's Guide.
+For example, you can use the following command to hide every track and set the knownGene track to +the pack visibiblity: +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.
+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). +
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&refSeqComposite_hideKids=1&ncbiRefSeqCurated=full&ncbiRefSeqCurated_sel=1
To jump directly to a gene's position on the Genome Browser, set the position parameter in the
-URL to a gene symbol (TP53, MTOR, KRAS, etc.) and add the
-parameter singleSearch=knownCanonical. For example, this link will open the
-Genome Browser for the hg19 human assembly at the position of the knownCanonical transcript
-associated with TP53:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position=TP53&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
+
+http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position=TP53
-You can also link directly to gene description pages from the URL. The following URL
-connecting to 'hgGene' will open up the Genome Browser description page
-containing funtion information, expression profile, and links to associated information for the above gene.
-Note the use of the URL parameter hgg_gene=:
http://genome.ucsc.edu/cgi-bin/hgGene?db=hg19&hgg_gene=TP53 &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.
+
+http://genome.ucsc.edu/cgi-bin/hgGene?db=hg19&hgg_gene=TP53
-You can combine the URL visibility settings with the hgct_customText= parameter using
+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 is an example of the hgct_customText URL variable:
hgct_customText URL variable, where
+"%20" is the URL encoding for spaces:
-Try the following example of the hgct_customText URL variable, note that the hub only has data -on chromosome 21: -
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigBed%20bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb+Try the following example of the hgct_customText URL variable. +
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigBed%20bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb
Similar to Custom Tracks, track hubs can be loaded into the URL usig the hubUrl=
-parameter. This parameter takes input similar to the Track Hub interface. Try the
-following example for reference:
http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt&genome=hg19- +
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 interface. Try the following example
+for reference:
http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt&db=hg19+ +
Hubs track visibility can also be changed from the URL parameters. The following link loads a +specific track from a supertrack with multiple composite subtracks.
+https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1>exRnaSignalMaleYoung_hideKids=1>exRnaSignalMaleYoung=full>exRnaSignalSRR1311243=full&ignoreCookie=1