How To Install chip-seq-data on Ubuntu 22.04
Introduction
In this tutorial we learn how to install chip-seq-data on Ubuntu 22.04.
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:
- 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.
This package contains the database files shipped with chip-seq.
There are three methods to install chip-seq-data on Ubuntu 22.04. 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 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-data using aptitude by running the following command:
sudo aptitude -y install chip-seq-data
How To Uninstall chip-seq-data on Ubuntu 22.04
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 Ubuntu 22.04, 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 Ubuntu 22.04 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
References
Summary
In this tutorial we learn how to install chip-seq-data package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
