22c8f329a95abd54770fbf6cc8d8d70c8c5149ee mspeir Mon Jan 6 13:49:01 2025 -0800 adding note about chromAlias, refs #26360 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index bda9cc9..877e29d 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -442,31 +442,35 @@ The data tracks provided by a hub must be formatted in one of the compressed binary index formats supported by the Genome Browser: <a href="bigWig.html">bigWig</a>, <a href="bigBed.html">bigBed</a>, <a href="bigGenePred.html">bigGenePred</a>, <a href="bigChain.html">bigChain</a>, <a href="bigNarrowPeak.html">bigNarrowPeak</a>, <a href="barChart.html">bigBarChart</a>, <a href="interact.html">bigInteract</a>, <a href="bigPsl.html">bigPsl</a>, <a href="bigMaf.html">bigMaf</a>, <a href="hic.html">hic</a>, <a href="bam.html">BAM</a>, <a href="cram.html">CRAM</a>, <a href="https://github.com/ComparativeGenomicsToolkit/hal" target="_blank">HAL</a> or -<a href="vcf.html">VCF</a>.</p> +<a href="vcf.html">VCF</a>. +Many of these formats also support several different <a +href="FAQcustom.html#custom12">chromosome aliases</a> (e.g. '1' or +'NC_000001.11' in place of 'chr1'). +</p> <p> <em>bigWig</em> - The bigWig format is best for displaying continuous value plot data, such as read depths from short read sequencing projects or levels of conservation observed in a multiple-species alignment. A bigWig file contains a list of chromosome segments, each of which is associated with a floating point value. When graphed, the segments may appear as a big "wiggle". Although each bigWig file can contain only a single value for any given base, bigWig tracks are often combined into "container multiWig" or "compositeTrack on" tagged tracks. For information on creating and configuring bigWig tracks, see the <a href="bigWig.html">bigWig Track Format</a> help page.</p> <p> <em>bigBed</em> - BigBed files are binary indexed versions of Browser Extensible Data (<a href="../../FAQ/FAQformat.html#format1">BED</a>) files. BED format is useful for associating a name and (optionally) a color and a score with one or more related regions on the same chromosome, such as all the exons of a gene. See the <a href="bigBed.html">bigBed Track Format</a> help page for information on creating and configuring bigBed tracks.</p>