3c1e958a16b6d79f859d0f51368d767acce0457c gperez2 Wed Jan 7 19:49:26 2026 -0800 Added some text and chromAlias/chromAuthority link to help pages, refs #33014 diff --git src/hg/htdocs/goldenPath/help/hubQuickStart.html src/hg/htdocs/goldenPath/help/hubQuickStart.html index c3ff77b99f5..9b630ff7bc0 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStart.html +++ src/hg/htdocs/goldenPath/help/hubQuickStart.html @@ -169,27 +169,32 @@ <a href="../help/examples/hubDirectory/hg19/trackDb.txt" target="_blank">example trackDb.txt</a>.</p> <p> When type is set to <b>bigBed</b>, the track hub assumes that the bigBed track is BED3 by default. To allow track hubs to use all fields in the bigBed file, one must define how many columns to expect. For example, if a bigBed file has nine columns, which would include an itemRgb field to display a R,G,B color value (e.g. 255,0,0), specify the type as <code>type bigBed 9</code>. If the file contains the first 9 <a href="../../FAQ/FAQformat.html#format1" target="_blank"> standard BED columns</a>, one could use <code>type bigBed 9 +</code> to denote the additional non-standard columns as defined in AutoSql format(.as) file, <code>-as=bedExample1.as</code>. </p> <p> Creating a trackDb.txt file for an assembly hub, you can control where the track appears underneath -the Genome Browser image using the <a href="/goldenpath/help/hgTrackHubHelp.html#groups" +the Genome Browser image using the <a href="/goldenPath/help/hgTrackHubHelp.html#groups" target="_blank">groups</a> setting. The special groups setting in Assembly Hubs points to a separate text document that defines track groups under the main image (such as the first "Mapping and Sequencing" group found on almost all Browsers). The group setting is not inherited by the subtracks for a composite, supertrack, or multiwigs, so you will have to add the setting to each stanza in the container. </p> - +<p> +Assembly hubs also support <a href="assemblyHubHelp.html#chromAlias" +target="_blank">chromAlias and chromAuthority</a>, which let the Browser map chromosome names +across different naming schemes and display a preferred convention. A default naming scheme can be +set using the <code>chromAuthority</code> setting. +</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->