---
name: "sga2wig"
section: "1"
platform: "linux"
package: "chip-seq"
version: "1.5.5-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sga2wig"
---

# sga2wig(1)

Convert SGA format into Wiggle Track format

## 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.