sga2bed command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

sga2bed: command not found

or when using sudo you get the following error message

sudo: sga2bed: command not found

Solutions to sga2bed: command not found

How To Fix sga2bed: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu sga2bed is provided by chip-seq package.

chip-seq is:

The ChIP-Seq software provides a set of tools performing common genome- wide ChIP- seq analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. These tools exist as stand-alone C programs and perform the following tasks:

1. Positional correlation analysis and generation of an aggregation plot (AP) (chipcor),
2. Extraction of specific genome annotation features around reference anchor points (chipextract),
3. Read centering or shifting (chipcenter),
4. Narrow peak caller using a fixed width peak size (chippeak),
5. Broad peak caller used for large regions of enrichment (chippart),
6. Feature selection tool based on a read count threshold (chipscore).

Because the ChIP-Seq tools are primarily optimized for speed, they use their own compact format for ChIP-seq data representation called SGA (Simplified Genome Annotation). SGA is a line-oriented, tab-delimited plain text format.

To fix this problem, we can install more using the command below.

sudo apt-get -y install chip-seq

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install chip-seq.

sudo apt -y install chip-seq

Or if you have aptitude installed you can use the following command.

sudo aptitude install chip-seq

Summary

In this tutorial we learn how to fix sga2bed command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.