- File format title
- Wiggle format (*.wig)
- Element type
- ru.biosoft.bsa (Bio-sequences analyses plugin)
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.
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:/ 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
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 1000 900 800 700 600 500 400 300 200 100