8ecb88fe6cfaf545b9d4e1eb67fd15cf5cb8ba72 dschmelt Tue May 14 15:09:17 2019 -0700 Made <input> format consistent, removed &s #23131 diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index aa7f0bd..d1f14dd 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -16,181 +16,183 @@ <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="#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.</p> +Tracks, Track Hubs, and Assembly Hubs. Note that the <input> format indicates a +user choice and not a valid example.</p> <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><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. 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><code>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&hgS_otherUserSessionName=<SessionName></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> +the <code>db=</code> and <code>position=</code> parameters. Note that the <input> +format indicates a user choice and not a valid example.</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> <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. Note that <em>italic text</em> indicates -a user choice, not a working example.</p> +parameters</a> section of the Custom Tracks User's Guide. Note that the <input> format indicates +a user choice and not a valid example.</p> <ul> <li><code>hideTracks=1</code> - hides all tracks</li> -<li><code><em>trackName</em>=hide|dense|pack|full</code> - sets specified track or subtrack to a +<li><code><trackName>=hide|dense|pack|full</code> - sets specified track or subtrack to a chosen visibility</li> -<li><code>textSize=<em>number</em></code> - sets browser text size to a chosen number, default of +<li><code>textSize=<number></code> - sets browser text size to a chosen number, default of 8 and maximum of 24</li> <li><code>ignoreCookie=1</code> - removes pre-existing user settings like track seletion, custom tracks, and track hubs</li> </ul> <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><code><em>trackName</em>_hideKids=1</code> - hides a specific composite track's subtracks</li> -<li><code><em>trackName</em>_sel=1</code> - selects specific subtrack to be 'checked', allowing +<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">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> -You can combine the URL visibility settings with the <code>&hgct_customText=</code> parameter using +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">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 +<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 +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=<em>araTha1</em></code>, where <em>araTha1</em> is the name set by +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> <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 +<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 +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. Creating <a href="../goldenPath/help/hgSessionHelp.html#Create">Saved Sessions</a> is the recommended way to share Genome Browser information.