2c91cdd0891e411d69bc5f0d0b920123e1c462eb kuhn Wed Aug 25 12:22:34 2021 -0700 added link to gene graphs page and simplified organization a bit, grouping getting started items in a list diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index 8db3df5..23cce7b 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -1,41 +1,45 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser User's Guide" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Genome Browser User Guide</h1> <h2>Contents</h2> <h6><a href="#What">What does the Genome Browser do?</a></h6> -<h6><a href="#GetStarted">Getting started: Genome Browser gateways</a></h6> <h6><a href="#FineTuning">Configuring the Genome Browser display</a></h6> <h6><a href="#IndivTracks">Annotation track descriptions</a></h6> <h6><a href="#BLATAlign">Using BLAT alignments</a></h6> -<h6><a href="#TableBrowser">Getting started on the Table Browser</a></h6> -<h6><a href="#Sessions">Getting started using Sessions</a></h6> -<h6><a href="#GenomeGraphs">Getting started on Genome Graphs</a></h6> -<h6><a href="#VisiGeneHelp">Using the VisiGene Image Browser</a></h6> +<h6>Getting Started with:</h6> +<ul> + <li> <h6><a href="#GetStarted">Genome Browser Gateway</a></h6> + <li> <h6><a href="#TableBrowser">Table Browser</a></h6> + <li> <h6><a href="#Sessions">Using Sessions</a></h6> + <li> <h6><a href="hgGeneGraph.html">Gene and Pathway Viewer</a></h6> + <li> <h6><a href="#GenomeGraphs">Genome Graphs</a></h6> +</ul> <h6><a href="#TrackFormatDNA">DNA text formatting</a></h6> <h6><a href="#Convert">Converting data between assemblies</a></h6> <h6><a href="#Download">Downloading genome data</a></h6> <h6><a href="#CustomTracks">Creating and managing custom annotation tracks</a></h6> <h6><a href="#TrackHubs">Getting started on Track Hubs</a></h6> -<h6><a href="#UseOneFile">Do Track Hubs require directories for the data?</a></h6> +<h6><a href="#UseOneFile">Track Hubs in a single file</a></h6> +<h6><a href="#VisiGeneHelp">Using the VisiGene Image Browser</a></h6> <hr> <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"> </p> </form> <form name="googleForm2" method="GET" action="http://www.google.com/search" onSubmit="document.googleForm2.q.value=document.googleForm2.qq.value+' site:genome.ucsc.edu/';"> <p> Search the entire Genome Browser website: @@ -1389,31 +1393,31 @@ Browser alongside native annotation tracks. Hubs are a useful tool for visualizing a large number of genome-wide data sets. The <a href="../../cgi-bin/hgHubConnect" target="_blank">Track Hub</a> utility allows efficient access to data sets from around the world through the familiar Genome Browser interface. Browser users can display tracks from any public track hub that has been registered with UCSC. Additionally, users can import data from unlisted hubs or can set up, display, and share their own track hubs.</p> <p> For information on using the Track Hub features, refer to the <a href="hgTrackHubHelp.html">Genome Browser Track Hub User Guide</a>. For specific information on configuring your trackDb.txt file, refer to the <a href="trackDb/trackDbHub.html">Track Database Definition Document</a>. See also the <a href="hubQuickStart.html" target="_blank">Basic Hub Quick Start Guide</a>, <a href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Track Hubs into Groupings</a>, <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs</a> and <a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable Track Hubs</a>.</p> <a name="UseOneFile"></a> -<h2>Do Track Hubs require directories for the data?</h2> +<h2>Track Hubs in a single file</h2> <p> Historically, a hub needed a set of text files to specify properties for a track hub and each of the data tracks within the hub. The track hub settings were stored in a three file structure: hub.txt, genomes.txt, and trackDb.txt</p> <pre> myHub/ - directory containing track hub files * hub.txt - a short description of hub properties * genomes.txt - list of genome assemblies included in the hub data * hg19/ - directory of data for the hg19 (GRCh37) human assembly ** trackDb.txt - display properties for tracks in this directory </pre> <p> Now, there is a trackDb option to have your entire track hub inside of one file, <code>useOneFile on</code>. Adding the <code>useOneFile on</code> line to the hub.txt section of the file allows the contents of all three files to be referenced inside of one file. We recommend the