Syntax

This tool converts wiggle data into interval type.

• Wiggle format: The .wig format is line-oriented. Wiggle data is preceeded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below.

  • 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
    

Example

• input wiggle format file:

  #track type=wiggle_0 name="Bed Format" description="BED format"
  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
  #track type=wiggle_0 name="variableStep" description="variableStep format"
  variableStep chrom=chr19 span=150
  59304701 10.0
  59304901 12.5
  59305401 15.0
  59305601 17.5
  #track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full
  fixedStep chrom=chr19 start=59307401 step=300 span=200
  1000
  900
  800
  700
  600
  

• convert the above file to interval file:

  chr19       59302000        59302300        +       -1.0
  chr19       59302300        59302600        +       -0.75
  chr19       59302600        59302900        +       -0.5
  chr19       59302900        59303200        +       -0.25
  chr19       59303200        59303500        +       0.0
  chr19       59304701        59304851        +       10.0
  chr19       59304901        59305051        +       12.5
  chr19       59305401        59305551        +       15.0
  chr19       59305601        59305751        +       17.5
  chr19       59307701        59307901        +       1000.0
  chr19       59308001        59308201        +       900.0
  chr19       59308301        59308501        +       800.0
  chr19       59308601        59308801        +       700.0
  chr19       59308901        59309101        +       600.0