9a051963c7dc7cafea316417701cae4570aff029 braney Sun Jul 13 13:07:07 2025 -0700 templates for bedMethyl and bigMethyl diff --git src/hg/htdocs/goldenPath/help/bigMethyl.html src/hg/htdocs/goldenPath/help/bigMethyl.html index 303624217bc..cd8cd4b6caa 100755 --- src/hg/htdocs/goldenPath/help/bigMethyl.html +++ src/hg/htdocs/goldenPath/help/bigMethyl.html @@ -1,81 +1,51 @@ - + -

BedMethyl Track Format

+

BigMethyl Track Format

-The bedMethyl format allows display of methylation sites. +The bigMethyl format allows display of methylation sites.

General Structure

-The bedMethyl format is line-oriented. BedMethyl data are preceded by a +The bigMethyl format is line-oriented. BigMethyl 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 18 column BED format:

chromA  chromStartA  chromEndA  dataValueA
 chromB  chromStartB  chromEndB  dataValueB
-

Parameters for bedMethyl track definition lines

+

Parameters for bigMethyl track definition lines

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
+
track type=bigMethyl name=track_label description=center_label
+

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 track type is REQUIRED, and must be bigMethyl:

+
type=bigMethyl

-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.)

Data Values

-BedMethyl track data values can be integer or real, positive or negative values. The +BigMethyl 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 +numerical order, and only the specified positions will be graphed. bigMethyl format has eighteen columns of data: 

chrom chromStart chromEnd dataValue

Example

-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 +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 validateFiles, outside of the browser.