fa8b8585e87d433f26deca1d476b122f1425ca96 kuhn Wed Feb 19 13:59:44 2020 -0800 added some hyphens where needed diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index c1dbeef..d800a4d 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -4,31 +4,31 @@ <!-- 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="zoomVariant">Zooming in or out using a link to ab HGVS identifier</a></li> <li><a href="#trackViz">Setting track visibility via 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="#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. In these examples, text in brackets <b>"<"</b> and <b>">"</b> indicate places where the user supplies information. Note that the brackets are not needed for the URL, including the brackets will result in a 'Could not find session' error.</p> @@ -194,31 +194,31 @@ 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=araTha1</code>, where araTha1 is the assembly 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="../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="../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> +<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, gene descriptions use the <code>hgg_gene=</code> 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. </p>