2bc4d4c29bb6270454b0945bb475f1b78bea0e08 braney Thu Jul 10 15:43:34 2025 -0700 some boiler plate for bedMethyl doc diff --git src/hg/htdocs/goldenPath/help/bedMethyl.html src/hg/htdocs/goldenPath/help/bedMethyl.html index dd8e700c9d2..303624217bc 100755 --- src/hg/htdocs/goldenPath/help/bedMethyl.html +++ src/hg/htdocs/goldenPath/help/bedMethyl.html @@ -1,44 +1,33 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser bedMethyl Track Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>BedMethyl Track Format</h1> <p> -The bedMethyl format allows display of continuous-valued data in track format. This display type is -useful for probability scores and transcriptome data. This track type is similar to the wiggle -(<a href="/goldenPath/help/wiggle.html">WIG</a>) format, but unlike the wiggle format, data exported -in the bedMethyl format are preserved in their original state. This can be seen on export using the -table browser. For more details on data compression in wiggle tracks see the notes section of the -wiggle <a href="wiggle.html" target="_blank">track description page</a>. If you have a very large -data set and you would like to keep it on your own server, you should use the <a href="bigWig.html"> -bigWig</a> data format. In fact, an attempt to load a bedMethyl custom track over 50,000,000 lines -will result in an error message, but can be addressed by turning the bedMethyl into a bigWig (see -<a href="bigWig.html#Ex3">Example 3</a>). Note that bedMethyl files cannot easily be converted to -wiggle files; converting bedMethyl to bigWig and using <code>bigWigToWig</code> will return the -original bedMethyl file.</p> +The bedMethyl format allows display of methylation sites. <h2>General Structure</h2> <p> The bedMethyl format is line-oriented. BedMethyl data are preceded by a <a href="customTrack.html#TRACK">track definition line</a>, which adds a number of options for controlling the default display of this track.</p> <p> -Following the track definition line are the track data in four column BED format:</p> +Following the track definition line are the track data in 18 column BED format:</p> <pre><code><em>chromA</em> <em>chromStartA</em> <em>chromEndA</em> <em>dataValueA</em> <em>chromB</em> <em>chromStartB</em> <em>chromEndB</em> <em>dataValueB</em></code></pre> <h3>Parameters for bedMethyl track definition lines</h3> <p> All options are placed in a single line separated by spaces:</p> <pre><code><strong>track type=</strong>bedMethyl <strong>name=</strong><em>track_label</em> <strong>description=</strong><em>center_label</em> <strong>visibility=</strong><em>display_mode</em> <strong>color=</strong><em>r,g,b</em> <strong>altColor=</strong><em>r,g,b</em> <strong>priority=</strong><em>priority</em> <strong>autoScale=</strong><em>on|off</em> <strong>alwaysZero=</strong><em>on|off</em> <strong>gridDefault=</strong><em>on|off</em> <strong>maxHeightPixels=</strong><em>max:default:min</em> <strong>graphType=</strong><em>bar|points</em> <strong>viewLimits=</strong><em>lower:upper</em> <strong>yLineMark=</strong><em>real-value</em> <strong>yLineOnOff=</strong><em>on|off</em> <strong>windowingFunction=</strong><em>maximum|mean|minimum</em> <strong>smoothingWindow=</strong>off|2-16</em></code></pre> <p> <strong>Note:</strong> if you copy/paste the above example, you must remove the line breaks.</p>