1914160557032a2cdb33aa9fd8cb548af5c19686 brianlee Mon Jan 6 15:24:28 2020 -0800 Adding a note on bedgraph.html about 50,000,000 line limit and bigWig suggestion refs #24729 diff --git src/hg/htdocs/goldenPath/help/bedgraph.html src/hg/htdocs/goldenPath/help/bedgraph.html index 0e2ef09..489e653 100755 --- src/hg/htdocs/goldenPath/help/bedgraph.html +++ src/hg/htdocs/goldenPath/help/bedgraph.html @@ -1,31 +1,33 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser bedGraph 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>BedGraph Track Format</h1> <p> The bedGraph 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 (WIG) format, but unlike the wiggle format, data exported in the bedGraph 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. +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 bedGraph custom track over 50,000,000 lines will result in an error message, +but can be addressed by turning the bedGraph into a bigWig (see <a href="bigWig.html#Ex3">Example 3</a>). Note that bedGraph files cannot easily be converted to wiggle files; converting bedGraph to bigWig and using <code>bigWigToWig</code> will return the original bedGraph file.</p> <h2>General Structure</h2> <p> The bedGraph format is line-oriented. BedGraph 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> <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 bedGraph track definition lines</h3>