b1dd32138ff6eb6a5ff7a9b55135abf3cd04bd69 dschmelt Mon Apr 29 16:56:28 2019 -0700 Various minor fixes for code review #23399, doc is still rough draft diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index 1d95dcb..6b77e79 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -1,167 +1,168 @@ <!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">Linking to the Genome Browser from another software application</a></li> -<li><a href="#link3">Linking to the browser at the position of a knownCanonical transcript +<li><a href="#link3">Linking to the Browser at the position of a knownCanonical transcript associated with a gene symbol</a></li> <li><a href="#link2">The <em>hgsid</em> parameter</a></li> <li><a href="#link4">Creating a custom URL to view specific tracks</a></li> <li><a href="#trackViz">Changing Track Visibilites with 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> </ul> <hr> <p> See also:</p> <ul> <li> The <a href="../../goldenPath/help/customTrack.html#optParams" target ="_blank">URL optional parameters</a> section of the Custom Tracks User's Guide.</p> <li> The <a href="https://en.wikipedia.org/wiki/UCSC_Genome_Browser#Customizing_direct_links" target="_blank">Customizing direct links</a> section of the UCSC Genome Browser wiki page.</p> <li><a href="index.html">FAQ Table of Contents</a></li> </ul> <a name="link1"></a> <h2>Linking to a specific position in the Genome Browser</h2> <p> You can make a link to a specific position in Genome Browser using a URL with the <code>db=</code> and <code>position=</code> parameters:</p> -<pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?db=[<em>db</em>]&position=[<em>position</em>]</code></pre> +<pre><code>../cgi-bin/hgTracks?db=[<em>db</em>]&position=[<em>position</em>]</code></pre> <p> Where:</p> <ul> <li> <em>db</em> - designates a specific assembly version. For example, to refer to the Feb. 2009 human release, you would use <code>db=hg19</code>. For a list of the db parameter values that correspond to UCSC assemblies, see the <a href="FAQreleases.html#release1">list of UCSC releases</a>.</li> <li><em>position</em> - can be any search value valid for the genome specified. 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> -<pre><a href=http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000</a></pre> +<pre><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></pre> <a name="link3"></a> -<h2>Linking to the browser on a particular gene symbol or displaying gene information</h2> +<h2>Linking to the Browser on a particular gene symbol or displaying gene information</h2> <p> Set the position parameter in the URL to the gene symbol and add the parameter <code>singleSearch=knownCanonical</code>. For example, this link will open the Genome Browser for the hg19 human assembly at the position of the knownCanonical transcript associated with GABRA3:</p> <pre><code><a href="../cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position=GABRA3" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&singleSearch=knownCanonical&position=GABRA3</a></code></pre> <p> The following URL connecting to 'hgGene' will open up the Genome Browser description page containing descriptions, expression, and links to associated information for the above gene. Note the use of the URL parameter <code>hgg_gene=</code>:</p> <pre><code><a href="../cgi-bin/hgGene?db=hg19&hgg_gene=GABRA3" target="_blank">http://genome.ucsc.edu/cgi-bin/hgGene?db=hg19&hgg_gene=GABRA3</a> </code></pre> <a name="link2"></a> <h2>The <em>hgsid</em> parameter</h2> <h6>What is the <em>hgsid</em> parameter? Should I include it in URLs when I make a link to the Genome Browser?</h6> <p> The <em>hgsid</em> parameter is a temporary, internally used parameter that stores information about what tracks the user last viewed, what position they were at, and what display settings they had enabled. This should not be used when constructing links to the Genome Browser and could unintentionally give someone access to private user data.</p> <a name="link3"></a> <h2>Creating a custom URL to view specific tracks</h2> <h6>How can I create a custom URL to view a specific subset of tracks in the Genome Browser?</h6> <p> Each assembly in the Genome Browser will display using a default set of tracks unless you specifically modify the track set in your URL. The easiest way to construct your custom 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">session</a>:</p> <ul> <li> Browse to the assembly of your choice (e.g. hg19).</li> <li> Click the "hide all" button. All tracks should now be hidden.</li> <li> Click the "My Data" pulldown in the blue navigation bar at the top of the screen to access Sessions.</li> <li> In the "Save Settings" section under "Save current settings as named session:", enter a name for your session.</li> <li> Check "allow this session to be loaded by others" if you want others to be able to access your session and URL.</li> <li> Click the "submit" button.</li> <li> Click the "Browser" link under "My Sessions" to open your session in the Browser. Your session URL should look similar to this: <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[<em>User Name</em>]&hgS_otherUserSessionName=[<em>Session Name</em>]</code></pre> <li> To display the tracks of your choice, simply add the names of the tables associated with the tracks to the end of the session URL in the format "&[table name]=[display mode]". For example, to add the Assembly track in full display mode, add the table name "&gold=full" to the end of the URL: <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[<em>User Name</em>]&hgS_otherUserSessionName=[<em>Session Name</em>]&gold=full </code></pre> If you don't know the table name for a track, in most cases you can view it by hovering the mouse cursor over either the gray bar to the left of the Browser's graphical display or the track's name in the group listings below the graphical display. In these cases the Browser will display a URL in the bottom left corner of the window, ending with the table name in the format "g=[table name]".</li> </ul> <p> Here is an example of a URL that displays the UCSC Genes track in pack mode and the RefSeq Genes in full mode: <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[<em>User Name</em>]&hgS_otherUserSessionName=[<em>Session Name</em>]&knownGene=pack&refGene=full </code></pre> <a name="trackViz"></a> <h2>Setting visibitlies via the URL</h2> <p> You can control the visibility of tracks via the URL with the following parameters, each linked by the & sign, similar to previous commands. Here are a few commands you can use -to control track visibility.</p> +to control track visibility. Note that <strong>bold text</strong> indicates a variable and not +actually an example.</p> <ul> <li>hideTracks=1</li> <li><strong>trackName</strong>=hide|dense|pack|full</li> <li>textSize=<strong>number</strong></li> <li>ignoreCookie=1</li> <li>position=chr1:250000-300000</li> <li>position=<strong>geneSymbol</strong>&singleSearch=knownCanonical</li> </ul> <p> For example, you can use the following command to only show the knownGene track:</p> -<pre>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack</pre> +<pre><a href=http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack</a></pre> <p>You can use the following command to go to a particular position: </p> -<pre>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:11000-20000</pre> +<pre><a href=http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:11000-20000>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:11000-20000</a></pre> <p>You can use the following command to go to a particular gene:</p> -<pre>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=KRAS&singleSearch=knownCanonical</pre> +<pre><a href=http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=KRAS&singleSearch=knownCanonical>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=KRAS&singleSearch=knownCanonical</a></pre> -<h2>Loading data using the URL</h2> +<h2>Loading data using a URL</h2> <a name="ctUrl"></a> <h3>Load Custom Track data with a URL</h3> <p> -You can combine the above URL settings with the <code>hgct_customText=</code> parameter, to input your track -line you would otherwise put in the <a href=http://genome.ucsc.edu/cgi-bin/hgCustom>custom track +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 hgct_customText URL variable:</p> -<pre>hgct_customText=track%20type=bigBed%20bigDataUrl=https://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</pre> <p> -Try the following example for reference, note that it only has data on chromosome 21: -<pre><a href=http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%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> +Try the following example of the hgct_customText URL variable, note that the hub only has data +on chromosome 21: +<pre><a href=../cgi-bin/hgTracks?db=hg38&hgct_customText=track%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> -<p>Similar to Custom Tracks, track hubs can be loaded into the URL usig the <code>hubURL=</code> -parameter. This parameter takes input similar to the <a href=http://genome.ucsc.edu/cgi-bin/hgHubConnect#unlistedHubs>Track Hub interface</a>. Try the +<p>Similar to Custom Tracks, track hubs can be loaded into the URL usig 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=http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt&genome=hg19>http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt&genome=hg19</a></pre> +<pre><a href=../cgi-bin/hgTracks?hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt&genome=hg19>http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt&genome=hg19</a></pre> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->