bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index fd47c9d4827..e13d50de0c7 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -776,32 +776,32 @@ data:</p> <ol> <li> The <b>species or genome assembly</b> 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=<databaseName></code>, where <em>databaseName</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=hg38 (Human Dec. 2013 assembly = GRCh38), db=mm10 (Mouse Dec. 2011 assembly = GRCm38).</li> <ul> <li>Additionally, particular genome assemblies, including assemblies in assembly hubs, can be specified using the <em>genome</em> parameter, <code>genome=<databaseName></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> + <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.gi.ucsc.edu/hubs/mouseStrains/hub.txt" + target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.gi.ucsc.edu/hubs/mouseStrains/hub.txt</a></li> </ul> <li> The <b>genome position</b> to which the Genome Browser should initially open. This information is of the form <code>position=<chrPosition></code>, where <em>chrPosition</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 <b>URL of the annotation file</b> on your web-accessible location. This information is of the form <code>hgt.customText=<url></code> or <code>hgct_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> </ol> <p> Combine the above pieces of information into a URL of the following format (the information @@ -824,31 +824,31 @@ <p> If you'd like to share your annotation track with a broader audience, send the URL for your track—along with a description of the format, methods, and data used—to the UCSC Genome mailing list <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. <!-- above address is genome at soe.ucsc.edu --> <a name="OPTIONAL"></a> <h3>Optional URL parameters</h3> <p> A special blog post discusses and provides examples of many of these parameters such as <code>hgct_customText=<url></code>, <code>db=<databaseName></code>, <code>hubUrl=<url></code>, and <code>genome=<databaseName></code> to attach custom tracks, track hubs, assembly hubs, and even track hubs to assembly hubs, all in a single URL. Read an overview of ways to share Genome Browser data views in the -<a href="https://genome-blog.soe.ucsc.edu/blog/2021/08/13/sharing-data-with-sessions-and-urls/" +<a href="https://genome-blog.gi.ucsc.edu/blog/2021/08/13/sharing-data-with-sessions-and-urls/" target="_blank">Sharing Data with Sessions and URLs</a> blog post. <a name="optParams"></a> <p> You can add other optional parameters to the URL: (Note: Display may vary if you have conflicting cart variables, for example having both hide all and highlight features.) <ul> <li> <code>guidelines=on/off</code> <br> activate or deactivate the blue guidelines <br>- <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&guidelines=off" target="_blank">example link</a> to switch off blue guidelines</li> <li>