9a051963c7dc7cafea316417701cae4570aff029 braney Sun Jul 13 13:07:07 2025 -0700 templates for bedMethyl and bigMethyl diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index f2a2506ed07..6e17315fdce 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -54,30 +54,31 @@ Format your data as a tab-separated file using one of the <a href="/FAQ/FAQformat.html" target="_blank">formats supported</a> by the Genome Browser. You may include more than one data set in your annotation file; these need not be in the same format. For many formats, chromosome names can either be UCSC-style names (e.g. 'chr1', 'chrX') or <a href="/FAQ/FAQcustom.html#custom12">aliases</a> from other sources (e.g. '1' or 'NC_000001.11'). Annotation data can be in a format designed specifically for the Human Genome Project or UCSC Genome Browser, including: <div class="container"> <div class="row"> <div class="col-xs-12 col-sm-6 col-md-2"> <ul> <li><a href="bigBed.html">bigBed</a></li> <li><a href="bigGenePred.html">bigGenePred</a> <li><a href="bigNarrowPeak.html">bigNarrowPeak</a> + <li><a href="bigMethyl.html">bigMethyl</a> <li><a href="bigMaf.html">bigMaf</a> <li><a href="bigChain.html">bigChain</a> </ul> </div> <div class="col-xs-12 col-sm-6 col-md-2"> <ul> <li><a href="bigPsl.html">bigPsl</a> <li><a href="barChart.html">barChart</a> <li><a href="barChart.html">bigBarChart</a> <li><a href="interact.html">interact</a> <li><a href="interact.html">bigInteract</a> </ul> </div> <div class="col-xs-12 col-sm-6 col-md-2"> <ul> @@ -523,30 +524,31 @@ enclosed in quotes if the text contains spaces. The default value is "User Supplied Track".</li> <li> <strong>type=<<em>track_type</em>></strong> <br> Defines the track type. The track type attribute is required for <a href="bam.html" target="_blank">BAM</a>, <a href="../../FAQ/FAQformat.html#format1.7" target="_blank">BED detail</a>, <a href="bedgraph.html" target="_blank">bedGraph</a>, <a href="barChart.html" target="_blank">bigBarChart</a>, <a href="bigBed.html" target="_blank">bigBed</a>, <a href="bigChain.html" target="_blank">bigChain</a>, <a href="bigGenePred.html" target="_blank">bigGenePred</a>, <a href="interact.html" target="_blank">bigInteract</a>, <a href="bigNarrowPeak.html" target="_blank">bigNarrowPeak</a>, + <a href="bigMethyl.html" target="_blank">bigMethyl</a>, <a href="bigMaf.html" target="_blank">bigMaf</a>, <a href="bigPsl.html" target="_blank">bigPsl</a>, <a href="bigWig.html" target="_blank">bigWig</a>, <a href="/FAQ/FAQformat.html#format13" target="_blank">broadPeak</a>, <a href="cram.html" target="_blank">CRAM</a>, <a href="interact.html" target="_blank">interact</a>, <a href="/FAQ/FAQformat.html#format12" target="_blank">narrowPeak</a>, <a href="/FAQ/FAQformat.html#format6.5" target="_blank">Microarray</a>, <a href="vcf.html" target="_blank">VCF</a> and <a href="wiggle.html" target="_blank">WIG</a> tracks.</li> <li> <strong>visibility=<<em>display_mode</em>></strong> <br> Defines the initial display mode of the annotation track. The numerical values or the words can be used, i.e., full mode may be @@ -1431,30 +1433,31 @@ <a name="EXAMPLE6"></a> <h3>Construct a sharable URL using the bigDataUrl setting</h3> <p> If you would like to share a URL that your colleague can click on directly, rather than loading it in the Custom Track tool (as in Example #5), then the URL will need a few extra parameters. Let's assume that your data is on a server at your institution in one of the large data formats: <a href="bigBed.html" target="_blank">bigBed</a>, <a href="bigWig.html" target="_blank">bigWig</a>, <a href="bigPsl.html" target="_blank">bigPsl</a>, <a href="barChart.html" target="_blank">bigBarChart</a>, <a href="bigChain.html" target="_blank">bigChain</a>, <a href="interact.html" target="_blank">bigInteract</a>, <a href="bigGenePred.html" target="_blank">bigGenePred</a>, <a href="bigMaf.html" target="_blank">bigMaf</a>, <a href="bigNarrowPeak.html" target="_blank">bigNarrowPeak</a>, +<a href="bigMethyl.html" target="_blank">bigMethyl</a>, <a href="bam.html" target="_blank">BAM</a>, <a href="cram.html" target="_blank">CRAM</a>, or <a href="vcf.html" target="_blank">VCF</a>. In this case, the URL must include an <code>hgct_customText</code> parameter, which simulates the text box on the Custom Tracks page. Also, the URL must include the <code>bigDataUrl</code> that points to the data file on your server. So, a clickable URL that opens a remote bigBed track for the hg18 assembly to a certain location on chr21 would look like this: <pre><code><a href="../../cgi-bin/hgTracks?db=hg18&position=chr21:33038447-33041505&hgct_customText=track%20type=bigBed%20name=myBigBedTrack%20description=%22a%20bigBed%20track%22%20visibility=full%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr21:33038447-33041505&hgct_customText<br> =track%20type=bigBed%20name=myBigBedTrack%20description=%22a%20bigBed%20track%22%20visibility=<br> full%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb </code></pre></a> <p> <strong>Tip:</strong> Multiple tracks can be placed into one custom track submission. To do so,