e1868c9f1dae8212b13ee13fdc785436ee7b7ff1 gperez2 Mon Nov 10 09:11:01 2025 -0800 Removing bigMethyl.html, we added the bigMethyl description in bedMethyl.html, No RM diff --git src/hg/htdocs/goldenPath/help/bigMethyl.html src/hg/htdocs/goldenPath/help/bigMethyl.html deleted file mode 100755 index cd8cd4b6caa..00000000000 --- src/hg/htdocs/goldenPath/help/bigMethyl.html +++ /dev/null @@ -1,51 +0,0 @@ -<!DOCTYPE html> -<!--#set var="TITLE" value="Genome Browser bigMethyl 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>BigMethyl Track Format</h1> -<p> -The bigMethyl format allows display of methylation sites. - -<h2>General Structure</h2> -<p> -The bigMethyl format is line-oriented. BigMethyl 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 bigMethyl track definition lines</h3> -<p> -All options are placed in a single line separated by spaces:</p> -<pre><code><strong>track type=</strong>bigMethyl <strong>name=</strong><em>track_label</em> <strong>description=</strong><em>center_label</em> - </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>bigMethyl</em>:</p> -<pre><code><strong>type=</strong>bigMethyl</code></pre> -<p> - -<h3>Data Values</h3> -<p> -BigMethyl 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. bigMethyl format has eighteen -columns of data: <pre><code><em>chrom chromStart chromEnd dataValue</em></code></pre></p> -<p> -<h2>Example</h2> -<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 bigMethyl data file to fail -validation by other tools, such as <code>validateFiles</code>, outside of the browser.</p> - -<!--#include virtual="$ROOT/inc/gbPageEnd.html" -->