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  Wiggle Track Format (WIG)
 

The wiggle (WIG) format allows display of continuous-valued data in track format. This display type is useful for GC percent, probability scores, and transcriptome data.

General Structure

The .wig format is line-oriented. Wiggle data are preceeded 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, which can be entered in several different formats described below. Three formats were developed to allow the file to be written most compactly, depending on the density of the data. When possible, please use the variableStep or fixedStep data types. The BED format is the most inefficient format and is not capable of loading as many data points as the other two formats.

  • BED format with no declaration line and four columns of data: 
      chromA  chromStartA  chromEndA  dataValueA
  chromB  chromStartB  chromEndB  dataValueB
  • variableStep two column data; started by a declaration line and followed with chromosome positions and data values: 
      variableStep  chrom=chrN  [span=windowSize]
  chromStartA  dataValueA
  chromStartB  dataValueB
  • fixedStep single column data; started by a declaration line and followed with data values: 
      fixedStep  chrom=chrN  start=position  step=stepInterval  [span=windowSize]
  dataValue1
  dataValue2

Parameters for 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
        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 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).

Data Values

Wiggle track data values can be integer or real, positive or negative values. Chromosome positions are specified as 1-relative. The first chromosome position is 1. The last position in a chromosome of length N would be 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.
  • The BED format is a subset of the previous description, with four columns of data: 
     chrom chromStart chromEnd dataValue
     Note: These BED coordinates are     zero-based, half-open, unlike the 1-relative coordinates for the variableStep and fixedStep formats.

    In many cases this format will be too verbose to conveniently specify a large number of data values. When possible, please use the variableStep or fixedStep data types. The BED format is the most inefficient format and is not capable of loading as many data points as the other two formats. Two other methods of specifying data were developed to be more space efficient.

  • The variableStep two column data format is the most commonly used data format. It begins with a declaration line: 
      variableStep chrom=chrN [span=windowSize]
     and is followed with two column data representing chromosome position and data value. The declaration line starts with the word variableStep and is followed by a specification for chromosome. The optional span allows more efficient encoding of a single value for a contiguous run of bases beginning at the specified position.

  • The fixedStep format takes a single column data, and is used when there is a regular interval between new data values. This is used for data values that apply to a constant size run of bases. The fixedStep single column data format begins with the declaration line: 
      fixedStep chrom=chrN start=chromStart step=stepInterval [span=windowSize]
     and is followed by a single column of data values. The declaration line starts with the keyword fixedStep, and it must include specifications for chrom, start, and step.

Example

This example specifies 28 separate data points in three tracks on chr19 in the region 59,302,001 to 59,311,000. 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 chr19:59302001-59311000
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 bed format
track type=wiggle_0 name="Bed Format" description="BED format" \
    visibility=full color=200,100,0 altColor=0,100,200 priority=20
chr19 59302000 59302300 -1.0
chr19 59302300 59302600 -0.75
chr19 59302600 59302900 -0.50
chr19 59302900 59303200 -0.25
chr19 59303200 59303500 0.0
chr19 59303500 59303800 0.25
chr19 59303800 59304100 0.50
chr19 59304100 59304400 0.75
chr19 59304400 59304700 1.00
#	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=255,200,0 \
    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 = 30 positions this as the third graph
#	Note, one-relative coordinate system in use for this format
track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full \
    autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 \
    graphType=points priority=30
fixedStep chrom=chr19 start=59307401 step=300 span=200
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Notes

For speed and efficiency, wiggle data is compressed and stored internally in 128 unique bins. This compression means that there is a loss of precision when the data is exported from a wiggle track (e.g. with output format "data points" or "bed format" within the table browser). The bedGraph format should be used instead if it is important to retain exact data when exporting.