.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH SGA2WIG "1" "March 2020" "sga2wig 1.5.5" "User Commands"
.SH NAME
sga2wig \- Convert SGA format into Wiggle Track format
.SH SYNOPSIS
.B sga2wig
[\fI\,options\/\fR] [\fI\,<\/\fR] \fI\,<SGA file|stdin>\/\fR
.SH DESCRIPTION
.IP
\- version 1.5.5
where options are:
.TP
\fB\-d\fR|\-\-debug
Produce Debug information
.TP
\fB\-h\fR|\-\-help
Show this Help text
.TP
\fB\-i\fR|\-\-db <path>
Use <path> to locate the chr_NC_gi and chr_size files
[default is: $HOME/db/genome]
.TP
\fB\-o\fR|\-\-format <0|1>
Set Wiggle Track data format: variableStep[def=0]/fixedStep[1]
.TP
\fB\-n\fR|\-\-chrnb
<int>         Chromosome number [def: 0 (all chromosomes)]
.TP
\fB\-b\fR|\-\-start
<int>         Chromosome start [def: \fB\-1\fR (entire chromosome)]
.TP
\fB\-e\fR|\-\-end
<int>         Chromosome end [def: \fB\-1\fR (entire chromosome)]
.TP
\fB\-c\fR|\-\-coff
<int>         Count cut\-off for the SGA input file [def=99999]
.TP
\fB\-s\fR|\-\-span
<int>         Wiggle Track Span(\fI\,/stepInterval\/\fP) parameter [def=150]
.IP
For fixedStep data format, it defines the step parameter
.TP
\fB\-f\fR|\-\-norm
<int>         Normalization factor for total tag counts within step intervals [def=0]
.IP
This option is only valid for fixedStep data format
.TP
\fB\-\-peakf\fR
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
.TP
\fB\-\-name\fR <name>
Set name for track name field [def. name=SGA\-feature]
.TP
\fB\-\-desc\fR <desc>
Set track description field [def. desc="ChIP\-Seq Custom data"]
.TP
\fB\-\-color\fR <col>
Define the track color in comma\-separated RGB values [def. 100,100,100]
.TP
\fB\-\-autoscale\fR
<on|off>     Data viewing paramenter: set auto\-scale to UCSC data view [def=OFF]
.TP
\fB\-\-always0\fR
<on|off>     Data viewing paramenter: always include zero [def=OFF]
.TP
\fB\-\-wfunction\fR
<func>       Data viewing paramenter: windowing function [def=mean+whiskers|maximum|mean|minimum]
.TP
\fB\-\-smoothing\fR
<grade>      Data viewing paramenter: smoothing window [def=OFF[0], <grade>=0,2..16]
.TP
\fB\-\-visibility\fR <mode>
Display mode: [def=full|dense|hide]
.IP
Convert SGA format into Wiggle Track format (WIG).
WIG format is line\-oriented, and is composed of declaration lines and data lines.
.IP
\- variableStep is for data with irregular intervals between new data points.
.IP
It begins with a declaration line and is followed by two columns containing chromosome positions and data values:
.TP
variableStep
chrom=chrN  [span=windowSize]
.TP
chromStartA
dataValueA
.TP
chromStartB
dataValueB
.TP
\&... etc ...
\&... etc ...
.IP
\- fixedStep is for data with regular intervals between new data values.
.IP
It begins with a declaration line and is followed by a single column of data values:
.TP
fixedStep
chrom=chrN  start=position  step=stepInterval  [span=windowSize = stepInterval]
.IP
dataValue1
dataValue2
\&... etc ...
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.