---
name: "sga2bed"
section: "1"
platform: "linux"
package: "chip-seq"
version: "1.5.5-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sga2bed"
---

# sga2bed(1)

Convert SGA format into BED format

## NAME

sga2bed - Convert SGA format into BED format

## SYNOPSIS

**sga2bed** \[*options*\] \[*\<*\] *\<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 file \[default is: $HOME/db/genome\]

- **-l**\|--readlen \<len\>

  Set Read length \<len\> Unoriented SGA files are extended by +/-\<len\>/2

- **-c**\|--score \<score\>

  Normalisation factor for BED score field (5th) \[score=1\]

- **-n**\|--norm

  \<normf\>        Normalisation factor for BED score field (7th) \[normf=1\]

- **-e**\|--extend f1:F1\[,f2:F2\] Set SGA optional field(s) f1(,f2,...) to BED field(s) F1,(F2,..)

  Fields are specified by column numbers Accepted BED field values are 4, 5, and 7 Except BED field 5 (score field), BED fields 4 and 7 can be used to set multiple extension values from SGA Fields 5 and 7 convert into numerical values whereas BED field 4 takes character strings as they are

- **-r**\|--nohdr

  BED format without annotation track header lines

- **-x**\|--expand

  Expand SGA lines into multiple BED lines

- **--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 \[def. 100,100,100\]

-

  Convert SGA format into BED format.

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.