9a051963c7dc7cafea316417701cae4570aff029 braney Sun Jul 13 13:07:07 2025 -0700 templates for bedMethyl and bigMethyl diff --git src/hg/htdocs/goldenPath/help/bedMethyl.html src/hg/htdocs/goldenPath/help/bedMethyl.html index 303624217bc..2b70c9ebc3f 100755 --- src/hg/htdocs/goldenPath/help/bedMethyl.html +++ src/hg/htdocs/goldenPath/help/bedMethyl.html @@ -12,70 +12,40 @@ <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 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> + </pre> <p> <strong>Note:</strong> if you copy/paste the above example, you must remove the line breaks.</p> <p> The track type is REQUIRED, and must be <em>bedMethyl</em>:</p> <pre><code><strong>type=</strong>bedMethyl</code></pre> <p> -The remaining values are OPTIONAL. The <a href="wiggle.html" target="_blank">wiggle</a> -documentation contains details on these options. A functional description of these options can be -seen in the <a href="hgWiggleTrackHelp.html" target="_blank">track configuration</a> description. -(Custom tracks do not have interactive configuration options.) <h3>Data Values</h3> <p> BedMethyl track data values can be integer or real, positive or negative values. The chromosome coordinates are <a href="../../FAQ/FAQtracks.html#tracks1">zero-based, half-open</a>. This means that the first chromosome position is 0, and the last position in a chromosome of length <em>N</em> would be <em>N - 1</em>. The positions listed in the input data must be in -numerical order, and only the specified positions will be graphed. bedMethyl format has four +numerical order, and only the specified positions will be graphed. bedMethyl format has eighteen columns of data: <pre><code><em>chrom chromStart chromEnd dataValue</em></code></pre></p> <p> <h2>Example</h2> <p> -This example specifies 9 separate data points in three tracks on chr19 in the region 49,302,001 to -49,304,701. To view this example as a custom track in the Genome Browser, copy the text and paste -it into the browser annotation track text box.</p> -<pre><code>browser position chr19:49302001-49304701 -browser hide all -browser pack refGene encodeRegions -browser full altGraph -# 300 base wide bar graph, autoScale is on by default == graphing -# limits will dynamically change to always show full range of data -# in viewing window, priority = 20 positions this as the second graph -# Note, zero-relative, half-open coordinate system in use for bedMethyl format -track type=bedMethyl name="BedMethyl Format" description="BedMethyl format" visibility=full color=200,100,0 altColor=0,100,200 priority=20 -chr19 49302000 49302300 -1.0 -chr19 49302300 49302600 -0.75 -chr19 49302600 49302900 -0.50 -chr19 49302900 49303200 -0.25 -chr19 49303200 49303500 0.0 -chr19 49303500 49303800 0.25 -chr19 49303800 49304100 0.50 -chr19 49304100 49304400 0.75 -chr19 49304400 49304700 1.00</code></pre> -<p> <strong>Note:</strong> The above example is a custom track that includes a <code>track type=</code> line that is specific for loading the data in the browser. This line will cause a raw bedMethyl data file to fail validation by other tools, such as <code>validateFiles</code>, outside of the browser.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->