How To Install chip-seq on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 457 words

Introduction

In this tutorial we learn how to install chip-seq on Ubuntu.

What is `chip-seq`

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:

Positional correlation analysis and generation of an aggregation plot (AP) (chipcor),
Extraction of specific genome annotation features around reference anchor points (chipextract),
Read centering or shifting (chipcenter),
Narrow peak caller using a fixed width peak size (chippeak),
Broad peak caller used for large regions of enrichment (chippart),
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.

There are three methods to install chip-seq on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install chip-seq Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install chip-seq using apt-get by running the following command:

sudo apt-get -y install chip-seq

Install chip-seq Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install chip-seq using apt by running the following command:

sudo apt -y install chip-seq

Install chip-seq Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install chip-seq using aptitude by running the following command:

sudo aptitude -y install chip-seq

How To Uninstall chip-seq on Ubuntu

To uninstall only the chip-seq package we can use the following command:

sudo apt-get remove chip-seq

Uninstall chip-seq And Its Dependencies

To uninstall chip-seq and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove chip-seq

Remove chip-seq Configurations and Data

To remove chip-seq configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge chip-seq

Remove chip-seq configuration, data, and all of its dependencies

We can use the following command to remove chip-seq configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge chip-seq

Dependencies

chip-seq have the following dependencies:

References

chip-seq website

Summary

In this tutorial we learn how to install chip-seq package on Ubuntu using different package management tools: apt, apt-get and aptitude.