5c20012735003a09af722339a7ea57f5cb827066 dschmelt Mon May 13 14:59:08 2019 -0700 Commiting minor changes for code review #23486, also adding more param lines to customTrack text #23459 diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index bc9c38a..e6ff50b 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -1,31 +1,31 @@

Frequently Asked Questions: Linking to the Genome Browser

Topics

Creating a sharable URL to view specific tracks

How do I create a link to the Genome Browser to share 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.

@@ -63,73 +63,73 @@ 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 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

    Setting Track Visibility via URL

    How do I create a custom URL to control the visibility of specific tracks?

    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 +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 hide every track (hideTracks=1) and set the knownGene track to the pack visibility (knownGene=pack):

    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
    +
    https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&refSeqComposite_hideKids=1&ncbiRefSeqCurated=full&ncbiRefSeqCurated_sel=1

    Loading data with the URL

    - +

    Loading Custom Track data with the URL

    How do I create a link to my custom track data?

    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:

    -
    http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb
    +
    http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr21:34821279-34888690&hgct_customText=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb

    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
    http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=browser%20position%20chr21:33038946-33039092%0Atrack%20type=bam%20bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam%20name=Example%20description=ExampleBAM

    More information on custom track parameters can be found in the Custom Track user guide.

    @@ -146,35 +146,35 @@

    Track hubs' track visibility can also be changed from the URL parameters. The following link specifies the hg19 genome database (db=hg19), loads a track hub (hubUrl=http), 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).

    https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1&gtexRnaSignalMaleYoung_hideKids=1&gtexRnaSignalMaleYoung=full&gtexRnaSignalSRR1311243=full&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 db=, you must use genome=araTha1, where araTha1 is the name set by your genomes.txt file in the line genome araTha1.

    https://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt

    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 +href="../goldenPath/help/hgTrackHubHelp.html">track hub user guide, +or the quick start guide to assembly hubs.

    Linking to gene specific information

    How do I link to a specific gene or specific gene description page?

    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

    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. Instead of a position search,