c5f99c872ca8a06458c33f93547e8b551556f48f brianlee Wed Jan 29 12:49:55 2020 -0800 Adding a doWiggle entry for custom track lines -and fixing a " needed in the page, refs #24857 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index 74041b0..7ca861a 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -591,31 +591,31 @@ <td>≤ 166</td> <td>167-277</td> <td>278-388</td> <td>389-499</td> <td>500-611</td> <td>612-722</td> <td>723-833</td> <td>834-944</td> <td>≥ 945</td></tr> </table><br> <li> <strong>group=<<em>group</em>></strong> - Defines the annotation track group in which the custom track will display in the Genome Browser window. By default, <em>group</em> is set to "user", which causes custom tracks to display at the top of the track listing in the - group "Custom Tracks". The value for "group" <strong>must</strong> be the + group "Custom Tracks". The value for "group" <strong>must</strong> be the "name" of one of the predefined track groups. To get a list of allowable group names for an assembly, go to the table browser and select "group: All Tables" "table: grp" and "get output" where entries in the "name" column may be used and some examples include "genes","regulation" and "rna".<br> (Note that mirrors may define other group names in the grp table and that the group setting does not work in track hubs, but does apply for assembly hubs.)</li> <li> <strong>priority=<<em>priority</em>></strong> - When the <em>group</em> attribute is set, defines the display position of the track relative to other tracks within the same group in the Genome Browser window. If <em>group</em> is not set, the <em>priority</em> attribute defines the track's order relative to other custom tracks displayed in the default group, "user".</li> <li> <strong>db=<<em>UCSC_assembly_name</em>></strong> - When set, indicates the specific genome assembly for which the annotation data is intended; the custom track manager will display an error if a user attempts to load the track onto a different assembly. Any valid UCSC assembly ID may be @@ -635,30 +635,40 @@ this track. This URL will be used in the details page for the track. Any "$$"in this string this will be substituted with the item name. There is no default for this attribute.</li> <li> <strong>htmlUrl=<<em>external_url</em>></strong> - Defines a URL for an HTML description page to be displayed with this track. There is no default for this attribute. A template for a standard format HTML track description is <a class="change" target="_blank" href="http://genome.ucsc.edu/goldenPath/help/ct_description.txt">here</a>.</li> <li> <strong>bigDataUrl=<<em>external_url</em>></strong> - Defines a URL to the data file for <a href="../help/bam.html" target="_blank">BAM</a>, <a href="../help/cram.html" target="_blank">CRAM</a>, <a href="../help/bigBed.html" target="_blank">bigBed</a>, <a href="../help/bigWig.html" target="_blank">bigWig</a> or <a href="../help/vcf.html" target="_blank">VCF</a> tracks. This is a required attribute for those track types. There is no default for this attribute.</li> + <li> + <strong>doWiggle=<<em>on</em>></strong> - The doWiggle setting enables BAM custom tracks + to be displayed as bar graphs where the height is proportional to the number of reads mapped + to each genomic position. This display is described as a density graph and is best viewed with + the track set to full and scaling set to auto-scale. See the Track Database Definition + <a href="../help/trackDb/trackDbHub.html#doWiggle" target="_blank">doWiggle entry</a> + for more information about the use in hubs and the + <a href="../help/hgBamTrackHelp" target="_blank">configuring BAM tracks</a> and the + <a href="../help/hgWiggleTrackHelp.html" target="_blank">configuring graph-based tracks</a> + help pages to learn how to further change the display.</li> </ul> <p> Here is an example of a properly formatted track line using the bigBed format, with accompanying browser line:</p> <pre><code>browser position chr21:33,031,597-33,041,570 track type=bigBed name="bigBed Example One" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</code></pre> <a name="SHARE"></a> <h2>Sharing your annotation track with others</h2> <p> To make your Genome Browser annotation track viewable by people on other machines or at other sites, follow the steps below.</p> <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>