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.