77b3375e4c19ea49971bc9f301c8ee13b401f974 brianlee Wed May 4 10:08:24 2022 -0700 Adding a link to blog post about sharing URLs in custom tracks user guide, refs #24314 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index 147a785..a219f60 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -686,34 +686,43 @@ <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> <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> <li> The genome position 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 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. + <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> </ul> +<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/" +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> - activate or deactivate the blue guidelines - <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> <code>hgFind.matches=<listOfNames></code> - highlight features given their names - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgFind.matches=uc010naf.1,uc011mcz.1" target="_blank">example link</a> to highlight two transcripts of the ABO gene</li> <li>