ddde745372e6f9aa3cb0d4e4fde7bece33eafa2e dschmelt Thu Sep 16 13:32:49 2021 -0700 Adding closing tags and breaks that were missing diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index a663ce6..5922a1d 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -32,31 +32,31 @@ </div> <div class="col-md-7"> <form name="googleForm1" method="GET" action="http://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+ ' site:genome.ucsc.edu/goldenPath/help';"> <p> Search the Genome Browser help pages: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=30 maxlength=255 value=""> <input type="submit" value="Submit"> </form> </p> -<p><a href="../../contacts.html">Questions and feedback are welcome</a>. +<p><a href="../../contacts.html">Questions and feedback are welcome</a>.</p> </div> </div> <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 @@ -121,31 +121,31 @@ Here is an example which opens the uniprot track at the default position for sacCer3:</p> <p><code><a href="/cgi-bin/hgTrackUi?db=sacCer3&g=uniprot&position=default">http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=sacCer3&g=uniprot&position=default</a></code></p> <a name="zoomVariant"></a> <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.out3=submit</code> zooms out 10x</li> <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 out 3x:</p> <p> <code><a href="../cgi-bin/hgTracks?db=hg19&position=NM_000257:c.1208G%3ET&hgt.out2=submit">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=NM_000257:c.1208G>T&hgt.out2=submit</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 @@ -169,55 +169,55 @@ parameters can be used individually or in combination.</p> <p><code><a href="../cgi-bin/hgTracks?db=hg38&ignoreCookie=1&hideTracks=1&mappability=full&umap24Quantitative.heightPer=100"> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&mappability=full&umap24Quantitative.heightPer=100</a></code></p> <p>Composite tracks have additional URL parameters that encode options to hide, select, and display subtracks.</p> <ul> <li><code><trackName>_hideKids=1</code> - hides a specific composite track's subtracks</li> <li><code><trackName>_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). +(ncbiRefSeqCurated_sel=1).</p> <pre><a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&refSeqComposite_hideKids=1&ncbiRefSeqCurated=full&ncbiRefSeqCurated_sel=1" target="_blank">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="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> If you have a custom track on a web-accessible server, you can use the location of the file to load it directly as part of a URL. 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&position=chr21:34821279-34888690&hgct_customText=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb" target="_blank">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: +equivalent input in the URL:</p> <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> <a name="hubUrl"></a> <h3>Loading Track Hubs and Assembly Hubs with the URL</h3> <h6>How do I create a link to my track hub or assembly hub?</h6> <p>Similar to custom tracks, track hubs can be loaded into the URL using the <code>hubUrl=</code> parameter. This parameter takes input similar to the <a href="../cgi-bin/hgHubConnect#unlistedHubs">track hub input box</a>. The following example @@ -323,33 +323,30 @@ <h3>Video demonstration: Links: Jump into genes </h3> <p> </p><p> <iframe width="560" height="315" src="https://www.youtube.com/embed/xmcyz2GyRKA?rel=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> Visit our <a href="https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" target="_blank">YouTube channel</a>. </p> <a name="LinkVid3"></a> -<p> -</p> +<br> <h3>Video demonstration: Links: Composites, custom tracks, spreadsheets</h3> +<br> <p> - <iframe width="560" height="315" src="https://www.youtube.com/embed/Yy4UmepYs2Q?rel=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> Visit our <a href="https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" target="_blank">YouTube channel</a>. -<p> -</p><p> - +</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->