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The wiggle (WIG) format is for display of dense, continuous data such as GC
percent, probability scores, and transcriptome data. Wiggle data elements must
be equally sized. If you need to display continuous data that is
sparse or contains elements of varying size, use the
BedGraph format instead.
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.
For speed and efficiency, wiggle data is compressed and stored internally in
128 unique bins. This compression means that there is a minor loss of precision
when data is exported from a wiggle track (i.e., with output format
"data points" or "bed format" within the table browser).
The bedGraph format should be used if it
is important to retain exact data when exporting.
See also:
Selecting a graphing track data format.
General Structure Wiggle format is line-oriented. For wiggle custom
tracks, the first line must be a track definition line, which
designates the track as a wiggle track and adds a number of options for
controlling the default display.
Wiggle format is composed of declaration lines and data lines. There are
two options for formatting wiggle data: variableStep and fixedStep.
These formats were developed to allow the file to be written as compactly as
possible.
Data Values
Wiggle track data values can be integer or real, positive or negative values.
Chromosome positions are specified as 1-relative. For a chromosome of length
N, the first position is 1 and the last position is N. Only positions
specified have data. Positions not specified do not have data and will not
be graphed. All positions specified in the input data must be in numerical
order.
Parameters for custom wiggle track definition lines
All options are placed in a single line separated by spaces:
track type=wiggle_0 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 have to remove the carriage returns.)
The track type with version is REQUIRED, and it currently must be wiggle_0:
type wiggle_0
The remaining values are OPTIONAL:
name trackLabel # default is "User Track"
description centerlabel # default is "User Supplied Track"
visibility full|dense|hide # default is hide (will also take numeric values 2|1|0)
color RRR,GGG,BBB # default is 255,255,255
altColor RRR,GGG,BBB # default is 128,128,128
priority N # default is 100
autoScale on|off # default is on
alwaysZero on|off # default is off
gridDefault on|off # default is off
maxHeightPixels max:default:min # default is 128:128:11
graphType bar|points # default is bar
viewLimits lower:upper # default is range found in data
yLineMark real-value # default is 0.0
yLineOnOff on|off # default is off
windowingFunction maximum|mean|minimum # default is maximum
smoothingWindow off|[2-16] # default is off
A functional description of these options can be seen in the Wiggle track configuration description.
(Custom tracks do not have interactive configuration options.)
Examples
This example specifies 19 separate data points in two tracks in the region
chr19:59,304,200-59,310,700. To view this example as a custom track in the
Genome Browser, copy the text and paste it
into the "Add Custom Tracks" text box.
browser position chr19:59304200-59310700
browser hide all
# 150 base wide bar graph at arbitrarily spaced positions,
# threshold line drawn at y=11.76
# autoScale off viewing range set to [0:25]
# priority = 10 positions this as the first graph
# Note, one-relative coordinate system in use for this format
track type=wiggle_0 name="variableStep" description="variableStep format" \
visibility=full autoScale=off viewLimits=0.0:25.0 color=50,150,255 \
yLineMark=11.76 yLineOnOff=on priority=10
variableStep chrom=chr19 span=150
59304701 10.0
59304901 12.5
59305401 15.0
59305601 17.5
59305901 20.0
59306081 17.5
59306301 15.0
59306691 12.5
59307871 10.0
# 200 base wide points graph at every 300 bases, 50 pixel high graph
# autoScale off and viewing range set to [0:1000]
# priority = 20 positions this as the second graph
# Note, one-relative coordinate system in use for this format
track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full \
autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 \
graphType=points priority=20
fixedStep chrom=chr19 start=59307401 step=300 span=200
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Caution for sparse variableStep data
The wiggle format was designed for quickly displaying data that is quite
dense. The variableStep format, in particular, becomes very inefficient when
there are only a few data points per 1,024 bases. If variableStep data points
(i.e., chromStarts) are greater than about 100 bases apart, it is
advisable to use BedGraph format.
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