69535d985db2e0cf42b05b5eaaae581704df5627 kuhn Thu Sep 9 18:03:41 2021 -0700 added search box, removed bullets from topics section to match other help pages, added section for videos about links diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index ca11811..a663ce6 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -1,268 +1,355 @@ <!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> +<div class="row"> +<div class="col-md-5"> +<h6> <a href="#link1">Creating a sharable URL to view specific tracks</a> </h6> +<h6> <a href="#link2">Linking to the Browser at a specific position, or default position</a> </h6> +<h6> <a href="#zoomVariant">Zooming in or out using a link to an HGVS identifier</a> </h6> +<h6> <a href="#trackViz">Setting track visibility via URL</a> </h6> +<h6> <a href="#custUrl">Loading Custom Tracks with the URL</a> </h6> +<h6> <a href="#hubUrl">Loading Track Hubs and Assembly Hubs with the URL</a> </h6> +<h6> <a href="#genes">Linking to gene-specific information</a> </h6> +<h6> <a href="#hgsid">The hgsid parameter</a> </h6> +<h6> <a href="#moreInfo">Additional URL parameters</a> </h6> + +<h6><a href="#Videos">Video demonstrations of making links</a></h6> <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, or default position</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="#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> + <li><a href="#LinkVid1"><strong> Understanding the URL</strong></a></li> + <li><a href="#LinkVid2"><strong> Jump into genes</strong></a></li> + <li><a href="#LinkVid3"><strong> Composites, custom tracks, spreadsheets</strong></a></li> + </ul> +</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>. + + </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 URL, including the brackets will result in a 'Could not find session' error.</p> <p> You will be able to share Genome Browser sessions with the following link format:</p> <p><code>http://genome.ucsc.edu/s/<userName>/<sessionName></code></p> <p> For instructions on creating a saved session, go to the <a href="../goldenPath/help/hgSessionHelp.html#Create" target ="_blank">session user guide</a>. If you want to specify track settings in a URL directly, please read the section on <a href="#trackViz">setting track visibility via URL</a> for a complete description. </p> <p> Or if you prefer the older style, which allows you to link to different tools, you may use the following format:</p> <p><code>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&gS_otherUserSessionName=<sessionName></code></p> <p> This longer format has the flexibility of replacing "hgTracks" with different tool names to share saved settings on the Table Browser (hgTables), Variant Annotation Integrator (hgVai), or Data Integrator (hgIntegrator). This will preserve your option selections and can be useful to share. The following format will bring the recipient to a user's custom Table Browser selections:</p> <p><code>http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&hgS_otherUserSessionName=<sessionName></code></p> <p>Both session link formats have the advantage of being able to add URL parameters to the end. The shorter link format requires a question mark before any URL parameters, with ampersand characters separating different parameters like so: </p> <p><code><a href=http://genome.ucsc.edu/s/view/clinicalzoom?textSize=18>http://genome.ucsc.edu/s/view/clinicalzoom?textSize=18</a></code></p> <p>Both formats require an ampersand between each additional parameter, seen in the longer format like so:</p> <p><code><a href=http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=view&hgS_otherUserSessionName=clinicalzoom&textSize=18>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=view&hgS_otherUserSessionName=clinicalzoom&textSize=18</a></code></p> <a name="link2"></a> <h2>Linking to the Browser at a specific position, or default position</h2> <h6>How do I make a link to a specific genome, position, or HGVS variant?</h6> <p> You can link to a specific genome assembly and position in the Genome Browser using a URL with the <code>db=</code> and <code>position=</code> parameters.</p> <p><code>http://genome.ucsc.edu/cgi-bin/hgTracks?db=<assembly>&position=<position></code></p> <p> Where:</p> <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> <h6>How do I make a link to the default position of a genome?</h6> <p> You can link directly to the default position of an assembly by passing the <code>position=default</code> parameter. This can be helpful in cases where a track exists on multiple assemblies, and you want to build links to each of them. If no position variable is passed, the Genome Browser assumes the default position for the default assembly (hg38).</p> <p> 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.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 the <a href="../goldenPath/help/customTrack.html#optParams" target ="_blank">optional URL parameters</a> section of the Custom Tracks User's Guide.</p> <ul> <li><code>hideTracks=1</code> - hides all tracks</li> <li><code><trackName>=hide|dense|pack|full</code> - sets specified track or subtrack to a chosen visibility</li> <li><code>textSize=<number></code> - sets browser text size to either 6, 8, 10, 12, 14, 18, 24, or 34. Default is a textSize of 12.</li> <li><code><trackName>.heightPer=<###></code> - sets a bigWig track's height to a particular number of pixels (between 20-100)</li> <li><code>ignoreCookie=1</code> - removes pre-existing user settings like track selection, custom tracks, and track hubs</li> </ul> <p> For example, you can use the following command to hide every track (hideTracks=1), set the genome database to hg38 (db=hg38), set the mappability track to full visibility (mappability=full), and set the umap track height to 100 pixels (umap24Quantitative.heightPer=100). Each of these 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). <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: <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 links to the hg19 genome database and an example track Hub:</p> <pre><a href=../cgi-bin/hgTracks?db=hg19&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt</a></pre> <p>Track hubs' track visibility can also be changed from the URL parameters. The following link specifies the genome database (db=hg19), loads a track hub (hubUrl=http.../hub.txt), 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=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, expression profile, and links to additional information for the gene TP53. </p> <p><code><a href="../cgi-bin/hgGene?db=hg19&hgg_gene=TP53" target="_blank">http://genome.ucsc.edu/cgi-bin/hgGene?db=hg19&hgg_gene=TP53</a> </code></p> <a name="hgsid"></a> <h2>The <em>hgsid</em> parameter</h2> <h6>What is the hgsid parameter and should I include it in Genome Browser links?</h6> <p>The hgsid is a temporary user ID that stores setting and custom track information in the URL. Including it in any shared URLs is a privacy concern, and it should be removed when constructing any links to the Genome Browser. Most significantly, it will change after you share it. Anyone using it will see that last thing you did, not what you thought you were sharing. Creating <a href="../goldenPath/help/hgSessionHelp.html#Create">Saved Sessions</a> is the recommended way to share Genome Browser information. </p> <a name="moreInfo"></a> <h2>Additional URL parameters</h2> <h6>Are there any more resources for URL and link parameters?</h6> <p> For more information, please see our <a href=../goldenPath/help/customTrack.html#optParams>section on URL parameters for custom tracks</a>. If you cannot find what you are looking for, please contact our active mailing list by emailing <a href="mailto:genome@soe.ucsc. edu">genome@soe.ucsc.edu</a>. All messages sent to that address are publicly archived. If your question includes sensitive data, you may send it instead to <a href="mailto:genome-www @soe.ucsc.edu"> genome-www@soe. ucsc.edu</a></p> + +<a name="Videos"></a> +<p> +</p> +<h2>Videos</h2> + +<a name="LinkVid1"></a> +<p> +</p> +<h3>Video demonstration: Links: Understanding the URL </h3> +<p> + +</p><p> +<iframe width="560" height="315" src="https://www.youtube.com/embed/p6TPvHDmpJk?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="LinkVid2"></a> +<p> +</p> +<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> +<h3>Video demonstration: Links: Composites, custom tracks, spreadsheets</h3> +<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> + + <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->