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The bigWig format is the recommended format for almost all graphing track needs (for more information, see the following wiki page). The wiggle (WIG) format is an older format for display of dense, continuous data such as GC percent, probability scores, and transcriptome data. Wiggle data elements must be equally sized. The bedGraph format is also an older format used to display sparse data or data that contains elements of varying size.
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.
Wiggle format is line-oriented. For wiggle custom tracks, the first line must be a track definition line (i.e., track type=wiggle_0), 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, and require a separate wiggle track definition line. 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.
This format is used for data with irregular intervals between new data points, and is the more commonly used wiggle format. After the wiggle track definition line, variableStep 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.
Caution about 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.
This format is used for data with regular intervals between new data values and is the more compact wiggle format. After the wiggle track definition line, fixedStep 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 1 is used. As the name suggests, fixedStep wiggles require the same size step throughout the dataset. If not specified, a step size of 1 is used.
Wiggle track data values can be integer or real, positive or negative values. 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.
BigWig files created from bedGraph format use "0-start, half-open" coordinates, but bigWigs that represent variableStep and fixedStep data are generated from wiggle files that use "1-start, fully-closed" coordinates. For example, for a chromosome of length N, the first position is 1 and the last position is N. For more information, see:
All options are placed in a single line separated by spaces (line breaks are inserted in the following example to facilitate readability):
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=mean+whiskers|maximum|mean|minimum smoothingWindow=off|2-16
The track type with version is REQUIRED, and it currently must be 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 color <RRR,GGG,BBB> # default is 255,255,255 altColor <RRR,GGG,BBB> # default is 128,128,128 priority <N> # default is 100
For a list of additional options, see the bigWig format page.
This example specifies 19 separate data points in two tracks in the region chr19:49,304,200-49,310,700. 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 chr19:49304200-49310700 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 49304701 10.0 49304901 12.5 49305401 15.0 49305601 17.5 49305901 20.0 49306081 17.5 49306301 15.0 49306691 12.5 49307871 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=49307401 step=300 span=200 1000 900 800 700 600 500 400 300 200 100