7f4c9f08fb12830d1c0b16ef96a21b38ae680cd7 jnavarr5 Mon May 20 17:20:18 2024 -0700 Making changes from Lou's code review, refs #33716 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index 740b0a0..4e2f266 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -1,29 +1,29 @@ <!-- This file contains custom track documentation included in --> <!-- hgTracksHelp.html and customTrack.html. --> <a name="CustomTracks"></a> <h2>What are custom annotation tracks?</h2> <p> The Genome Browser provides dozens of aligned annotation tracks that have been computed at UCSC or have been provided by outside collaborators. In addition to these standard tracks, it is also possible for users to upload their own annotation data for temporary display in the browser. These custom annotation tracks are viewable only on the machine from which they were uploaded and are automatically discarded 48 hours after the last time they are accessed, unless they are saved in a <a href="/goldenPath/help/hgSessionHelp.html#CTs" target="_blank">Session</a>. Optionally, users can make custom annotations viewable by others as well. For a more stable option for custom annotations, we suggest using <a href="hgTrackHubHelp.html" target="_blank">track hubs</a>. A third, more -technical, option is to operate a mirror. Custom tracks work well for quickly displaying data, while +technical option, is to operate a mirror. Custom tracks work well for quickly displaying data, while track hubs are more configurable and permanent.</p> <p> Custom tracks are a wonderful tool for research scientists using the Genome Browser. Because space is limited in the Genome Browser track window, many excellent genome-wide tracks cannot be included in the standard set of tracks packaged with the browser. Other tracks of interest may be excluded from distribution because the annotation track data is too specific to be of general interest or can't be shared until journal publication. In the past, many individuals and labs contributed custom tracks to the Genome Browser website for use by others. For historical purposes, a <a href="../customTracks/custTracks.html" target="_blank">list of these custom annotation tracks</a> is available. </p> <p> Track hubs are now the preferred approach for viewing and sharing data on the Browser. Labs, consortia, and institutions submit their hubs to be listed as a <a href="hgTrackHubHelp.html#View" target="_blank">Public Hub</a>. Track hubs require remotely hosted data. They use binary index @@ -41,32 +41,31 @@ <li><a href="#BROWSER">Browser lines</a></li> <li><a href="#TRACK">Track lines</a></li> <li>Data lines</li> </ul> <a name="CREATE"></a> <h3>Building and sharing a custom track</h3> <p> To construct an annotation file and display it in the Genome Browser, follow these steps:</p> <a name="format"></a> <p> <strong>Step 1. Format the data set</strong><br> Format your data as a tab-separated file using one of the <a href="/FAQ/FAQformat.html" target="_blank">formats supported</a> by the Genome -Browser. Chromosome references must be of the form <em>chrN</em> (the parsing of chromosome names -<em><strong>is</strong></em> case-sensitive). You may include more than one data set in your +Browser. You may include more than one data set in your annotation file; these need not be in the same format. Annotation data can be in a format designed specifically for the Human Genome Project or UCSC Genome Browser, including: <div class="container"> <div class="row"> <div class="col-xs-12 col-sm-6 col-md-2"> <ul> <li><a href="bedgraph.html">bedGraph</a> <li><a href="/FAQ/FAQformat.html#format4">GTF</a> and <a href="/FAQ/FAQformat.html#format3">GFF</a> <li><a href="/FAQ/FAQformat.html#format2">PSL</a> <li><a href="/FAQ/FAQformat.html#format1">BED</a> <li><a href="wiggle.html">WIG</a> </ul> </div> <div class="col-xs-12 col-sm-6 col-md-2"> @@ -404,48 +403,41 @@ <A HREF="../../cgi-bin/hgTables" TARGET=_blank>Table Browser</A>, select the correct genome assembly, then select the track name from the <em>track</em> list. The <em>table</em> list will show the primary table. Alternatively, the primary table name can be obtained from a mouseover on the track name in the track control section. You can also find instructions on how to find this table name in the video "<a href="../../training/vids/index.html#vid06" target="_blank">How do I learn which tables belong to a data track on the UCSC Genome Browser?</a>".</p> <p> Note that composite track subtracks are not valid <em>track_primary_table_name</em> values. To find the symbolic name of a composite track, look in the <em>tableName</em> field in the <em>trackDb</em> table, or mouse over the track name in the track control section. It is not possible to display only a subset of the subtracks at this time.</p> <p> Definition: <strong><em><track_primary_table_name(s)></em></strong>. You can find the primary -table name by clicking "View Table Schema" from the track's description page, or from the -Table Browser. It will be listed as the Primary Table. Alternatively, you can mouse-over the track -label in the Browser and look at the URL the link points to. The part after the g= in the URL is the -track's primary table name (e.g., for UCSC Genes you will see g=knownGene in the URL. The track -primary table is knownGene).</p> +table name by clicking "Data format description" from the track's description page, or +from the Table Browser. It will be listed as the Primary Table. Alternatively, you can mouse-over +the track label in the Browser and look at the URL the link points to. The part after the g= in the +URL is the track's primary table name (e.g., for UCSC Genes you will see g=knownGene in the URL. +The track primary table is knownGene).</p> <ul> <li> <strong>position <<em>position</em>></strong> <br> Determines the part of the genome that the Genome Browser will initially open to, in chromosome:start-end format.</li> -<!-- - <li> - <strong>pix <<em>width</em>></strong> - <br> - Sets the Genome Browser window to the specified width in - pixels.</li> ---> <li> <strong>hide all</strong> <br> Hides all annotation tracks except for those listed in the custom track file.</li> <li> <strong>hide <<em>track_primary_table_name(s)</em>></strong> <br> Hides the listed tracks. Multiple track names should be space-separated.</li> <li> <strong>dense all</strong> <br> Displays all tracks in dense mode. NOTE: Use the "all" option cautiously. If the browser display includes a large number of tracks or a large position @@ -797,32 +789,32 @@ db=hg38 (Human Dec. 2013 assembly = GRCh38), db=mm10 (Mouse Dec. 2011 assembly = GRCm38).</li> <ul> <li>Additionally, particular genome assemblies, including assemblies in assembly hubs, can be specified using the <em>genome</em> parameter, <code>genome=<databaseName></code>, which acts in the same manner as the <em>db</em> parameter. Here is an example using the house mouse (<i>Mus musculus</i>, 129S1_SvImJ) assembly hub: <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt</a></li> </ul> <li> The <b>genome position</b> to which the Genome Browser should initially open. This information is of the form <code>position=<chrPosition></code>, where <em>chrPosition</em> is a chromosome number, with or without a set of coordinates. Examples of this include: position=chr22, position=chr22:15916196-31832390.</li> <li> - The <b>URL of the annotation file</b> on your web site. This information is of the form - <code>hgt.customText=<url></code> or <code>hgct_customText=<url></code>, + The <b>URL of the annotation file</b> on your web-accessible location. This information is of the + form <code>hgt.customText=<url></code> or <code>hgct_customText=<url></code>, where <em>url</em> points to the annotation file on your website. An example of an annotation file URL is <a href="test.bed" target="_blank">http://genome.ucsc.edu/goldenPath/help/test.bed</a>.</li> </ol> <p> Combine the above pieces of information into a URL of the following format (the information specific to your annotation file is highlighted):</p> <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?org=<font color="000099"><em><organismName></em></font>&position=<font color="000099"><em><chrPosition></em></font>&hgt.customText=<font color="000099"><em><url></em></font></code></pre> <p> <strong>Step 3. Provide the URL to others</strong></p> <p> If you created a <a href=../help/hgSessionHelp.html>session</a>, that stable link can be freely shared.</p> <p> Otherwise, to upload a custom annotation track from a URL into the Genome Browser, paste the URL into the large