+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
+(WIG) 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 track description page. If you have a very large
+data set and you would like to keep it on your own server, you should use the
+bigWig 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
+Example 3). Note that bedMethyl files cannot easily be converted to
+wiggle files; converting bedMethyl to bigWig and using bigWigToWig will return the
+original bedMethyl file.
+The bedMethyl format is line-oriented. BedMethyl data are preceded by a +track definition line, which adds a number of options for +controlling the default display of this track.
++Following the track definition line are the track data in four column BED format:
+ +chromA chromStartA chromEndA dataValueA
+chromB chromStartB chromEndB dataValueB+All options are placed in a single line separated by spaces:
+track type=bedMethyl name=track_label description=center_label
+ visibility=display_mode color=r,g,b altColor=r,g,b
+ priority=priority autoScale=on|off alwaysZero=on|off gridDefault=on|off
+ maxHeightPixels=max:default:min graphType=bar|points viewLimits=lower:upper
+ yLineMark=real-value yLineOnOff=on|off
+ windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16+Note: if you copy/paste the above example, you must remove the line breaks.
++The track type is REQUIRED, and must be bedMethyl:
+type=bedMethyl+The remaining values are OPTIONAL. The wiggle +documentation contains details on these options. A functional description of these options can be +seen in the track configuration description. +(Custom tracks do not have interactive configuration options.) + +
+BedMethyl track data values can be integer or real, positive or negative values. The +chromosome coordinates are zero-based, half-open. +This means that the first chromosome position is 0, and the last position in a chromosome +of length N would be N - 1. The positions listed in the input data must be in +numerical order, and only the specified positions will be graphed. bedMethyl format has four +columns of data:
chrom chromStart chromEnd dataValue+
+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.
+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
+Note:
+The above example is a custom track that includes a track type= 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 validateFiles, outside of the browser.