sga2wig - Convert SGA format into Wiggle Track format
sga2wig [options] [<] <SGA
file|stdin>
- - 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 ...
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.