How To Install chip-seq-data on Kali Linux

Introduction

In this tutorial we learn how to install chip-seq-data on Kali Linux.

What is chip-seq-data

chip-seq-data 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.

This package contains the database files shipped with chip-seq.

There are three methods to install chip-seq-data on Kali Linux. 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-data 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-data using apt-get by running the following command:

sudo apt-get -y install chip-seq-data

Install chip-seq-data Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install chip-seq-data

Install chip-seq-data Using aptitude

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

sudo aptitude update

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

sudo aptitude -y install chip-seq-data

How To Uninstall chip-seq-data on Kali Linux

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

sudo apt-get remove chip-seq-data

Uninstall chip-seq-data And Its Dependencies

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

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

Remove chip-seq-data Configurations and Data

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

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

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

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

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

Dependencies

chip-seq-data have the following dependencies:

References

• chip-seq-data website

Summary

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