cd5a9cb6994919e931d32d43bed2ad149e87c62c dschmelt Wed May 8 11:09:54 2019 -0700 Adding more info and changes from Brian's proofread #23131 diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index 0943684..1bdacca 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -1,157 +1,209 @@ <!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="#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="#trackViz">Changing Track Visibility via URL</a></li> -<li><a href="#ctUrl">Adding Custom Tracks via URL</a></li> -<li><a href="#hubUrl">Connection to a Track Hub via URL</a></li> -<li><a href="../goldenPath/help/customTrack.html#optParams">Additional URL parameters</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 data, Custom Tracks, and -Track Hubs.</p> +Saved sessions are a versatile way to share data that may include native annotations, Custom +Tracks, Track Hubs, and Assembly Hubs.</p> <p> -You will be able to save and share Genome Browser sessions with the following format: -<p><code>http://genome.ucsc.edu/s/<em>userName</em>/<em>sessionName</em></code></p></p> -<p> -Or if you prefer a modifiable, longer URL; use this format:</p> -<p><code>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[<em>UserName</em>]&hgS_otherUserSessionName=[<em>SessionName</em>]</code></p> +You will be able to share Genome Browser sessions with the following link format: +<p><code>http://genome.ucsc.edu/s/<em>userName</em>/<em>sessionName</em></code></p> <p> For instructions on creating a saved session, go to the -<a href="../goldenPath/help/hgSessionHelp.html#Create">Saved Session Help page</a>.</p> -<p> +<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">changing track visibility via URL</a> for a complete description. -Note that these URL parameters do not work with the shorter session URLs. +<a href"#trackViz">setting track visibility via URL</a> for a complete description. +Note that URL parameters do not work with the shorter session URLs. </p> + +<p> +Or if you prefer a modifiable, longer URL; use the following format:</p> +<p><code>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[<em>UserName</em>]&hgS_otherUserSessionName=[<em>SessionName</em>]</code></p> +<p>It has the advantage of being able to add additional URL parameters to the end and the +flexibility of replacing "hgTracks" with different tools 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.</p> <a name="link2"></a> <h2>Linking to the Browser at a specific position</h2> <h6>How do I make a link to a specific genome or position?</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=[<em>db</em>]&position=[<em>position</em>]</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> - -<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. Creating -<a href="../goldenPath/help/hgSessionHelp.html#Create">Saved Sessions</a> is the recommended way to -share Genome Browser information. -</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 Visibitlies via URL</h2> +<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 commands. For the full list, please see the +each linked by the "&" sign, similar to position parameters. For the full list, please see 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>hideTracks=1</li> <li><em>trackName</em>=hide|dense|pack|full</li> <li>textSize=<em>number</em></li> +<li>ignoreCookie=1</li> </ul> <p> -For example, you can use the following command to hide every track and set the knownGene track to -the pack visibility:</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> +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><em>trackName</em>_hideKids=1</li> <li><em>trackName</em>_sel=1</li> -<li>ignoreCookie=1</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> + +<h2>Loading data with the URL</h2> +<a name="ctUrl"></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> + +<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 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/"> +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 +to assembly hubs</a>. + <a name="link3"></a> -<h2>Linking to the Browser to get gene information</h2> -<h6>How do I link to a specific gene or specific gene description page?</h6><p> +<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> -<h2>Loading data using a URL</h2> -<a name="ctUrl"></a> -<h3>Load Custom Track data with a 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 is an example of the <code>hgct_customText</code> URL variable, where -"%20" is the URL encoding for spaces:</p> -<p> -Try the following example of the hgct_customText URL variable. -<pre><a href=../cgi-bin/hgTracks?db=hg38&hgct_customText=browser%20position=chr1%20track%20type=bigBed%20bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigBed%20bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</a></pre> -</p> - -<a name="hubUrl"></a> -<h3>Load a Track Hub with a 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 interface</a>. Try the following example -for reference:</p> -<pre><a href=../cgi-bin/hgTracks?hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt&db=hg19>http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt&db=hg19</a></pre> -<p>Hubs track visibility can also be changed from the URL parameters. The following link loads a -specific track from a supertrack with multiple composite subtracks.</p> -<pre><a href"https://genome.ucsc.edu/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> +<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. 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> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->