f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f gperez2 Fri Sep 26 17:46:49 2025 -0700 Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index d22d7f638c4..3300cd5bfd1 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -19,32 +19,31 @@ <h6><a href="#Search">Setting up item search</a></h6> <h6><a href="#Filters">Adding filters to your Track Hub</a></h6> <h6><a href="#Register">Registering a Track Hub with UCSC</a></h6> <h6><a href="#Compatibility">Checking Hub settings and compatibility</a></h6> <h6><a href="#Hosting">Where to host your data</a></h6> <h6><a href="https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html" target = _blank>Track Hub Database Definition Document</a></h6> <hr> <p> <strong>Additional resources</strong></p> <ul> <li>Raney BJ, et al. <a href="https://doi.org/10.1093/bioinformatics/btt637" target="_blank">Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser</a>. <em>Bioinformatics</em>. 2014 Apr 1;30(7):1003-5. <li> - <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly Hubs - Wiki</a></li> + <a href="assemblyHubHelp.html" target="_blank">Assembly Hub User Guide</a></li> <li> <a href="trackDb/trackDbHub.html" target="_blank">Track Database Definition Document</a> (Reference guide for trackDb parameter definitions)</li> <li><a href="https://genome-blog.soe.ucsc.edu/blog/2022/06/28/track-hub-settings/" target= "_blank">Track hub settings blog post</a></li> <li> <a href="publicHubGuidelines.html" target="_blank">Public Hub Guidelines</a></li> <li> <a href="hubQuickStart.html" target="_blank">Quick Start Guide to Basic Hubs</a></li> <li> <a href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Track Hubs into Groupings</a></li> <li> <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs with Blat</a></li> @@ -113,32 +112,32 @@ the persistence of their data, or would like to take full advantage of track functionality, or create a browser on sequence not natively supported by UCSC or a genome browser mirror, track hubs are a better solution. Both mechanisms give data providers the flexibility to directly add, update, and remove data from their display as needed.</p> <!-- ========== What Are Assembly Hubs? ============================== --> <a name="Assembly"></a> <h2>What Are Assembly Hubs?</h2> <p> Assembly Data Hubs extend the functionality of Track Data Hubs to assemblies that are not hosted natively on the Browser. Assembly Data Hubs were developed to address the increasing need for researchers to annotate sequence for which UCSC does not provide an annotation database. They allow researchers to include the underlying reference sequence, as well as data tracks that annotate that sequence. Sequence is stored in the UCSC twoBit format, and the annotation tracks are stored in the same manner as Track Data Hubs. For more information on how to setup your own Assembly Data Hub, -please refer to the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs">Assembly Hub -wiki</a> and see the <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to +please refer to the <a href="assemblyHubHelp.html">Assembly Hub User Guide</a> and see the +<a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs</a>.</p> <!-- ========== Viewing Hub Tracks in the Browser ==================== --> <a name="View"></a> <h2>Viewing Track Hubs</h2> <h3>Public hubs</h3> <p> The Genome Browser provides links to a collection of public track hubs that have been registered with UCSC. To view a list of the public track hubs available, click into the blue navigation bar "My Data" and then "Track Hubs" to reach the <a href="../../cgi-bin/hgHubConnect?#publicHubs">Public Track Hubs page</a>. You can click links in the "Description" column to see details about a particular Hub. To view a hub's data, click on an assembly name on the row of your hub or the "Connect" button. If you clicked the "Connect" button, choose your assembly or click the "Genome Browser" link from the top blue bar to be brought to the