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.

sga2wig 1.5.5                                      March 2020                                         SGA2WIG(1)