9ab80f9387e6e46cb1a19f85b3b696e915d8a62f kuhn Sun May 17 18:09:44 2020 -0700 made zoomVariant link in index work by adding hashtag, fixed a typo, changed header of HGVS section to better match the index. adding new anchor tag, genes, for linking to gene names that is more descriptive, leaving the original link3 in place in case anyone outside links to it (we do not). weirdly, there is already an anchor in the doc called gene that is not used anywhere I can find diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index d800a4d..337296d 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -1,34 +1,34 @@ <!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="zoomVariant">Zooming in or out using a link to ab HGVS identifier</a></li> +<li><a href="#zoomVariant">Zooming in or out using a link to an 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="#genes">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> @@ -71,31 +71,31 @@ <ul> <li> <code>db</code> - designates a specific genome assembly. For example, <code>db=hg19</code> refers to the Feb. 2009 human genome release. For a list of db parameter values that 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="zoomVariant"></a> -<h2>Zooming in or out with a link</h2> +<h2>Zooming in or out with a link — HGVS </h2> <h6>How do I zoom out using a link to a HGVS identifier?</h6> <p> To link to a specific HGVS identifier, you can construct a link with the HGVS identifier in the position field instead of coordinates. The default padding is 5bp on either side, but you can always zoom in or out with <code>hgt.out1=submit</code> or <code>hgt.in1=submit</code>. The numbers 1 through 4 zoom in or out corresponding to the buttons above the track window. The following lists the zoom levels of each number, applicable to zooming in or out:</p> <ul> <li><code>hgt.out1=submit</code> zooms out 1.5x</li> <li><code>hgt.out2=submit</code> zooms out 3x</li> <li><code>hgt.out3=submit</code> zooms out 10x <li><code>hgt.out4=submit</code> zooms out 100x</li> </ul> <p> The following link is an example which leads to the variant NM_00257:c.1208G>T and zooms @@ -193,30 +193,31 @@ <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=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="genes"></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, 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,