Difference between revisions of "Wiggle format"

Latest revision as of 16:40, 17 May 2013

File format title

Wiggle format (*.wig)

Element type

track

Plugin

ru.biosoft.bsa (Bio-sequences analyses plugin)

[edit] Description

Wiggle format (WIG) allows the display of continuous-valued data in a track format.

WIG 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.

variableStep is for data with irregular intervals between new data points and is the more commonly used wiggle format. It begins with a declaration line and is followed by two columns containing chromosome positions and data values:

variableStep  chrom=chrN  [span=windowSize]
chromStartA  dataValueA
chromStartB  dataValueB
... etc ...  ... etc ...

The declaration line starts with the word variableStep and is followed by a specification for a chromosome. The optional span parameter (default: span=1) allows data composed of contiguous runs of bases with the same data value to be specified more succinctly. The span begins at each chromosome position specified and indicates the number of bases that data value should cover. For example, this variableStep specification:

variableStep chrom=chr2
300701 12.5
300702 12.5
300703 12.5
300704 12.5
300705 12.5

is equivalent to:

variableStep chrom=chr2 span=5
300701 12.5

Both versions display a value of 12.5 at position 300701-300705 on chromosome 2.

fixedStep is for data with regular intervals between new data values and is the more compact wiggle format. It begins with a declaration line and is followed by a single column of data values:

fixedStep  chrom=chrN  start=position  step=stepInterval  [span=windowSize]
dataValue1
dataValue2
... etc ...

The declaration line starts with the word fixedStep and includes specifications for chromosome, start coordinate, and step size. The span specification has the same meaning as in variableStep format. For example, this fixedStep specification:

fixedStep chrom=chr3 start=400601 step=100
11
22
33

displays the values 11, 22, and 33 as single-base regions on chromosome 3 at positions 400601, 400701, and 400801, respectively. Adding span=5 to the declaration line:

fixedStep chrom=chr3 start=400601 step=100 span=5
11
22
33

causes the values 11, 22, and 33 to be displayed as 5-base regions on chromosome 3 at positions 400601-400605, 400701-400705, and 400801-400805, respectively. Note that for both variableStep and fixedStep formats, the same span must be used throughout the dataset. If no span is specified, the default span of one is used.

[edit] 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.

[edit] 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:/ the track type with version is required. 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

[edit] Example

This example specifies 19 separate data points in two tracks in the region chr19:59,304,200-59,310,700.

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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[edit] References

1. http://genome.ucsc.edu/goldenPath/help/wiggle.html