b9835eeed840bf68dd1d425a45c7d2f70ec3b4f9 dschmelt Tue Nov 17 14:01:06 2020 -0800 CR edits refs #26543 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 015bc0e..f4caf49 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -5,31 +5,31 @@ <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Using UCSC Genome Browser Track Hubs</strong></h1> <h2>Contents</h2> <h6><a href="#Intro">What Are Track Hubs?</a></h6> <h6><a href="#Assembly">What Are Assembly Hubs?</a></h6> <h6><a href="#View">Viewing Track Hubs</a></h6> <h6><a href="#Sharing">Sharing Track Hubs</a></h6> <h6><a href="#Setup">Setting up a Track Hub</a></h6> <h6><a href="#Debug">Debugging Track Hubs</a></h6> <h6><a href="#Search">Setting up item search</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="#Compatibility">Checking Hub settings and compatibility</a></h6> <h6><a href="#Hosting">Where to host your data</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> <li> <a href="trackDb/trackDbHub.html" target="_blank">Track Database Definition Document</a> (Reference guide for trackDb parameter definitions)</li> <li> @@ -167,34 +167,34 @@ <h2>Sharing Track Hubs</h2> <p>When sharing track hubs on a single assembly, we recommend using <a href="../../cgi-bin/hgSession">Saved Sessions</a> (especially for publications). These have the advantages of being single-click access and sharing a full browser configuration. If you are just starting, an overview of the process is to make the hub on your web-accessible server, attach the hub to the Genome Browser, configure browser position and related tracks, then <a href="../../cgi-bin/hgSession"> save your named session</a> and share the session link. Your session links will be in the following format with your chosen username and session name:</p> <ul> <li><a href="http://genome.ucsc.edu/s/ExampleUser/TrackHubSession"> http://genome.ucsc.edu/s/ExampleUser/TrackHubSession</a></li> </ul> -<p>We have additional resources about Saved Session -<a href="hgSessionHelp.html#HowToShare" target="_blank">sharing</a> and -<a href="hgSessionHelp.html#Create" target="_blank"> -backup to a file</a>.</p> +<p>For additional information, see <a href="hgSessionHelp.html#HowToShare">sharing Saved Sessions +</a> and +<a href="hgSessionHelp.html#Create"> +backing up custom data</a>.</p> <p> If you prefer URL manipulation, it is also possible to add or <a href="../../FAQ/FAQlink.html#hubUrl" target="_blank">share a track hub directly by URL</a> or otherwise <a href="../help/customTrack.html#optParams" target="_blank">modify the browser via URL</a>. For example, if you add <strong>hubUrl=[URL]</strong> to your hgTracks URL line, it will add the hub directly into the browser:</p> <ul> <li><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt"> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt</a></li></ul> <p> If you are adding an assembly hub with multiple genomes, you can link directly to hgGateway, the assembly selection page and a particular genome:</p> <ul> <li><a href="../../cgi-bin/hgGateway?genome=GCF_000699105.1&hubUrl=https://hgdownload.soe.ucsc.edu/hubs/birds/hub.txt">