---
name: "bed2sga"
section: "1"
platform: "linux"
package: "chip-seq"
version: "1.5.5-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bed2sga"
---

# bed2sga(1)

Convert BED format into SGA format.

## NAME

bed2sga - Convert BED format into SGA format.

## SYNOPSIS

**bed2sga** \[*options*\] \[*-s \<s\_assembly (e.g. hg19)\>*\] \[*\<*\] *\<BED 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 assembly-specific chr\_NC\_gi file \[default is: $HOME/db/genome\]

- **-f**\|--feature \<ft\>

  Set Feature name \<ft\>

- **-s**\|--species \<spec\>

  Assembly \<spec\> (i.e hg19)

- **-c**\|--center

  Generate a Centered SGA file

- **-u**\|--unoriented

  Generate an unoriented SGA file

- **-r**\|--regional

  Generate a 2-line\[+/-\] SGA file representing BED regions (e.g. RepeatMasker regions)

- **-e**\|--extend \<f1,f2,...\>

  Produce an extended SGA file with additional fields specified by a comma-separated list of BED column numbers (from 1 to n)

- **--useScore**

  Use the BED 'score' field (#5) to set the SGA 'count' field

- **--useSigVal**

  Use the BED 'Signal Value' field (#7) to set the SGA 'count' field \[This option is only valid for ENCODE narrowPeak\]

- **--narrowPeak**

  Use this option for ENCODE narrowPeak format \[Options **--useScore**, **-c**, and **-u** are ignored\]

-

  Convert BED format into SGA format.

## AUTHOR

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