780fb29b38481270113febeaee49b8e30d8e8a61 ccpowell Thu Aug 15 13:38:26 2019 -0700 Editing the genome= section to customtracktext.html page, refs #22069 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index cc7cda5..fa77b09 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -662,31 +662,31 @@ <p> <strong>Step 1.</strong> Put your formatted annotation file on your web site. Be sure that the file permissions allow it to be read by others.</p> <p> <strong>Step 2.</strong> Construct a URL that will link this annotation file to the Genome Browser. The URL must contain 3 pieces of information specific to your annotation data:</p> <ul> <li> The species or genome assembly on which your annotation data is based. To automatically display the most recent assembly for a given organism, set the <em>org</em> parameter: <em>e.g.</em> <code>org=human</code>. To specify a particular genome assembly for an organism, use the <em>db</em> parameter, <code>db=database_name</code>, where <em>database_name</em> is the UCSC code for the genome assembly. For a list of these codes, see the Genome Browser <a href="/FAQ/FAQreleases.html#release1" target="_blank">FAQ</a>. Examples of this include: db=hg16 (Human July 2003 assembly), db=mm6 (Mouse Mar. 2005 assembly).</li> - <li>Additionally, a particular genome assembly, including assembly hubs, can be specified using + <li>Additionally, particular genome assemblies, including assemblies in assembly hubs, can be specified using the <em>genome</em> parameter, <code>genome=database_name</code>, which acts in the same manner as the <em>db</em> parameter. Here is an example using the house mouse (<i>Mus musculus</i>, 129S1_SvImJ) assembly hub: <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt</a></li> <li> The genome position to which the Genome Browser should initially open. This information is of the form <code>position=chr_position</code>, where <em>chr_position</em> is a chromosome number, with or without a set of coordinates. Examples of this include: position=chr22, position=chr22:15916196-31832390.</li> <li> The URL of the annotation file on your web site. This information is of the form <code>hgt.customText=URL</code>, where <em>URL</em> points to the annotation file on your website. An example of an annotation file URL is <a href="test.bed" target="_blank">http://genome.ucsc.edu/goldenPath/help/test.bed</a>.</li>