How To Install tophat on Ubuntu 18.04

In this tutorial we learn how to install tophat on Ubuntu 18.04. tophat is fast splice junction mapper for RNA-Seq reads

Introduction

In this tutorial we learn how to install tophat on Ubuntu 18.04.

What is tophat

tophat is:

TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology.

There are three methods to install tophat on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install tophat Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install tophat

Install tophat Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install tophat using apt by running the following command:

sudo apt -y install tophat

Install tophat 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 tophat using aptitude by running the following command:

sudo aptitude -y install tophat

How To Uninstall tophat on Ubuntu 18.04

To uninstall only the tophat package we can use the following command:

sudo apt-get remove tophat

Uninstall tophat And Its Dependencies

To uninstall tophat and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:

sudo apt-get -y autoremove tophat

Remove tophat Configurations and Data

To remove tophat configuration and data from Ubuntu 18.04 we can use the following command:

sudo apt-get -y purge tophat

Remove tophat configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge tophat

References

Summary

In this tutorial we learn how to install tophat package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.