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SGA2WIG(1) User Commands SGA2WIG(1)

NAME

sga2wig - Convert SGA format into Wiggle Track format

SYNOPSIS

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

DESCRIPTION

- version 1.5.5 where options are:
Produce Debug information
Show this Help text
Use <path> to locate the chr_NC_gi and chr_size files [default is: $HOME/db/genome]
Set Wiggle Track data format: variableStep[def=0]/fixedStep[1]
<int> Chromosome number [def: 0 (all chromosomes)]
<int> Chromosome start [def: -1 (entire chromosome)]
<int> Chromosome end [def: -1 (entire chromosome)]
<int> Count cut-off for the SGA input file [def=99999]
<int> Wiggle Track Span(/stepInterval) parameter [def=150]
For fixedStep data format, it defines the step parameter
<int> Normalization factor for total tag counts within step intervals [def=0]
This option is only valid for fixedStep data format
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
Set name for track name field [def. name=SGA-feature]
Set track description field [def. desc="ChIP-Seq Custom data"]
Define the track color in comma-separated RGB values [def. 100,100,100]
<on|off> Data viewing paramenter: set auto-scale to UCSC data view [def=OFF]
<on|off> Data viewing paramenter: always include zero [def=OFF]
<func> Data viewing paramenter: windowing function [def=mean+whiskers|maximum|mean|minimum]
<grade> Data viewing paramenter: smoothing window [def=OFF[0], <grade>=0,2..16]
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:
chrom=chrN [span=windowSize]
dataValueA
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:
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.

March 2020 sga2wig 1.5.5