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 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser FAQ" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Frequently Asked Questions: Linking to the Genome Browser</h1> <h2>Topics</h2> <ul> <li><a href="#link1">Creating a sharable URL to view specific tracks</a></li> <li><a href="#link2">Linking to the Browser at a specific position</a></li> <li><a href="#trackViz">Setting track visibility via URL</a></li> -<li><a href="#ctUrl">Loading Custom Tracks with the URL</a></li> +<li><a href="#custUrl">Loading Custom Tracks with the URL</a></li> <li><a href="#hubUrl">Loading Track Hubs and Assembly Hubs with the URL</a></li> <li><a href="#link3">Linking to gene specific information</a></li> <li><a href="#hgsid">The hgsid parameter</a></li> <li><a href="#moreInfo">Additional URL parameters</a></li> </ul> <a name="link1"></a> <h2>Creating a sharable URL to view specific tracks</h2> <h6>How do I create a link to the Genome Browser to share my data?</h6> <p> The easiest way to save and share tracks from the URL is by <a href="../cgi-bin/hgLogin" TARGET="_blank">logging in</a> to your Genome Browser account and creating a <a href="../goldenPath/help/hgSessionHelp.html">saved session</a>. Saved sessions are a versatile way to share data that may include native annotations, Custom Tracks, Track Hubs, and Assembly Hubs.</p> @@ -63,73 +63,73 @@ correspond to UCSC assemblies, see the <a href="FAQreleases.html#release1">list of UCSC releases</a>.</li> <li><code>position</code> - can be any search term for the genome specified, including a position range or a gene identifier. This often takes the form of <code>position=chr1:35000-40000</code>.</li> </ul> <p>The following link is an example of a URL that declares assembly and position:</p> <p><code><a href="../cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000</a></code></p> <a name="trackViz"></a> <h2>Setting Track Visibility via URL</h2> <h6>How do I create a custom URL to control the visibility of specific tracks?</h6> <p> 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 <a href="../../goldenPath/help/customTrack.html#optParams" target ="_blank">optional URL +the <a href="../goldenPath/help/customTrack.html#optParams" target ="_blank">optional URL parameters</a> section of the Custom Tracks User's Guide. Note that <em>italic text</em> indicates a user choice, not a working example.</p> <ul> <li><code>hideTracks=1</code> - hides all tracks</li> <li><code><em>trackName</em>=hide|dense|pack|full</code> - sets specified track or subtrack to a chosen visibility</li> <li><code>textSize=<em>number</em></code> - sets browser text size to a chosen number, default of 8 and maximum of 24</li> <li><code>ignoreCookie=1</code> - removes pre-existing user settings like track seletion, custom tracks, and track hubs</li> </ul> <p> 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):</p> <p><code><a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack</a></code></p> <p>Composite tracks have additional URL parameters that encode options to hide, select, and display subtracks.</p> <ul> <li><code><em>trackName</em>_hideKids=1</code> - hides a specific composite track's subtracks</li> <li><code><em>trackName</em>_sel=1</code> - selects specific subtrack to be 'checked', allowing display</li> </ul> <p>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). -<pre><a href="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</a></pre> +<pre><a href="../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</a></pre> <h2>Loading data with the URL</h2> -<a name="ctUrl"></a> +<a name="custUrl"></a> <h3>Loading Custom Track data with the URL</h3> <h6>How do I create a link to my custom track data?</h6> <p> You can combine the URL visibility settings with the <code>&hgct_customText=</code> parameter using a track line you would otherwise put in the <a href="../cgi-bin/hgCustom">custom track input box</a>. The following example shows the <code>hgct_customText</code> parameter accepting a bigBed file URL as a custom track: </p> -<pre><a href="../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&hgct_customText=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</a></pre> +<pre><a href="../cgi-bin/hgTracks?db=hg38&position=chr21:34821279-34888690&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</a></pre> <p> If you want to add more information to the Custom Track, you can do so using the <code>hgct_customText</code> 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 <a href="../cgi-bin/hgCustom">custom track input box</a> and the equivalent input in the URL: <pre>browser position chr21:33038946-33039092 track type=bam bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam name=Example description=ExampleBAM</pre> <pre><a href="../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">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</a></pre> <p> More information on custom track parameters can be found in the <a href="../goldenPath/help/customTrack.html">Custom Track user guide</a>.</p> @@ -146,35 +146,35 @@ <p>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).</p> <pre><a href="../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">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</a></pre> <p> 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 <code>db=</code>, you must use <code>genome=<em>araTha1</em></code>, where <em>araTha1</em> is the name set by your genomes.txt file in the line <code>genome araTha1</code>.</p> <pre><a href=../cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt>https://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt</a></pre> <p> To see the files behind that assembly hub, please visit the -<a href="http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/"> +<a href="../goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/"> hub's directory</a>. For more information on assembly hubs in general, please see the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target ="_blank">assembly hub wiki</a>, the <a -href="http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html">track hub user guide</a>, -or the <a href=http://genome.ucsc.edu/goldenPath/help/hubQuickStartAssembly.html>quick start guide +href="../goldenPath/help/hgTrackHubHelp.html">track hub user guide</a>, +or the <a href=../goldenPath/help/hubQuickStartAssembly.html>quick start guide to assembly hubs</a>. <a name="link3"></a> <h2>Linking to gene specific information</h2> <h6>How do I link to a specific gene or specific gene description page?</h6> <p> 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 <code>&singleSearch=knownCanonical</code>. For example, the following link will open the Genome Browser for the hg19 human assembly at the position of TP53 on the knownCanonical dataset </p> <p><code><a href="../cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position=TP53" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position=TP53</a></code></p> <p> <a name="gene"></a> You can also link directly to gene description pages from the URL. Instead of a position search,