26021fdf598718825035c26faae8acca18f818eb jnavarr5 Fri Nov 7 11:47:26 2025 -0800 Documenting that the group setting needs to be in each stanza for a container, refs #35079 #34995 diff --git src/hg/htdocs/goldenPath/help/hubQuickStart.html src/hg/htdocs/goldenPath/help/hubQuickStart.html index 09620cec5ae..c3ff77b99f5 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStart.html +++ src/hg/htdocs/goldenPath/help/hubQuickStart.html @@ -167,20 +167,29 @@ also allows for advanced <a href="trackDb/trackDbHub.html#groupingTracks" target="_blank">track grouping</a> known as composites, superTracks and multiWigs. See a basic <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" +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> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->