NAME

       sga2wig - Convert SGA format into Wiggle Track format

SYNOPSIS

       sga2wig [options] [<] <SGA file|stdin>

DESCRIPTION

              - version 1.5.5 where options are:

       -d|--debug
              Produce Debug information

       -h|--help
              Show this Help text

       -i|--db <path>
              Use <path> to locate the chr_NC_gi and chr_size files [default is: $HOME/db/genome]

       -o|--format <0|1>
              Set Wiggle Track data format: variableStep[def=0]/fixedStep[1]

       -n|--chrnb
              <int>         Chromosome number [def: 0 (all chromosomes)]

       -b|--start
              <int>         Chromosome start [def: -1 (entire chromosome)]

       -e|--end
              <int>         Chromosome end [def: -1 (entire chromosome)]

       -c|--coff
              <int>         Count cut-off for the SGA input file [def=99999]

       -s|--span
              <int>         Wiggle Track Span(/stepInterval) parameter [def=150]

              For fixedStep data format, it defines the step parameter

       -f|--norm
              <int>          Normalization  factor  for  total  tag  counts within step intervals
              [def=0]

              This option is only valid for fixedStep data format

       --peakf
              Indicate that the The SGA input file represents a peak file [i.e.  coordinates  are
              peak  centers]  In  such  case,  the  span  range  begins upstream of [span=]150 bp
              chromosome position specified, and ends [span=]150 bp downstream

       --name <name>
              Set name for track name field [def. name=SGA-feature]

       --desc <desc>
              Set track description field [def. desc="ChIP-Seq Custom data"]

       --color <col>
              Define the track color in comma-separated RGB values [def. 100,100,100]

       --autoscale
              <on|off>     Data viewing paramenter: set auto-scale to UCSC data view [def=OFF]

       --always0
              <on|off>     Data viewing paramenter: always include zero [def=OFF]

       --wfunction
              <func>            Data      viewing      paramenter:       windowing       function
              [def=mean+whiskers|maximum|mean|minimum]

       --smoothing
              <grade>         Data    viewing    paramenter:    smoothing   window   [def=OFF[0],
              <grade>=0,2..16]

       --visibility <mode>
              Display mode: [def=full|dense|hide]

              Convert SGA format into Wiggle Track format (WIG).  WIG  format  is  line-oriented,
              and is composed of declaration lines and data lines.

              - variableStep is for data with irregular intervals between new data points.

              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 ...

              - fixedStep is for data with regular intervals between new data values.

              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 = stepInterval]

              dataValue1 dataValue2 ... etc ...

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.