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/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index 48086be95a9..1ca48ee863e 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -338,31 +338,31 @@ (hideTracks=1), hides the subtrack kids of a particular track (gtexRnaSignalMaleYoung_hideKids=1), sets a specific subtrack to be displayed (gtexRnaSignalSRR1311243=full), and ignores user settings (ignoreCookie=1).</p> <pre><a href="../cgi-bin/hgTracks?db=hg19&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1>exRnaSignalMaleYoung_hideKids=1>exRnaSignalMaleYoung=full>exRnaSignalSRR1311243=full&ignoreCookie=1">https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1&gtexRnaSignalMaleYoung_hideKids=1&gtexRnaSignalMaleYoung=full&gtexRnaSignalSRR1311243=full&ignoreCookie=1</a></pre> <p> To link to an assembly hub and display data on a non-natively supported genome, the same parameters apply. To specify the intended genome assembly, instead of using <code>db=</code>, you must use <code>genome=araTha1</code>, where araTha1 is the assembly name set by your genomes.txt file in the line <code>genome araTha1</code>.</p> <pre><a href=../cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt>https://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt</a></pre> <p> To see the files behind that assembly hub, please visit the <a href="../goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/"> hub's directory</a>. For more information on assembly hubs in general, please see the -<a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target ="_blank">assembly hub wiki</a>, the <a +<a href="../goldenPath/help/assemblyHubHelp.html" target ="_blank">assembly hub user guide</a>, the <a href="../goldenPath/help/hgTrackHubHelp.html">track hub user guide</a>, or the <a href=../goldenPath/help/hubQuickStartAssembly.html>quick start guide to assembly hubs</a>. </p> <h6 id="hubClear">Use <code>hubClear=</code> to remove hubs at the same location</h6> <p> Another feature one can use in place of <code>hubUrl=</code> is <code>hubClear=</code>, which will load a hub while simultaneously disconnecting or clearing, hubs located at the same location. For example, adding <code>hubClear=http://university.edu/lab/folder/hub10.txt</code> would connect the referenced hub10.txt while simultaneously disconnecting any hubs that might be displayed from the same <code>http://university.edu/lab/folder/</code> directory (for example, hub1.txt, hub2.txt, etc.). This feature can be useful for dynamically generated hubs that might collect in the browser otherwise. </p>