How To Install rsem on Debian 10

Learn how to install rsem on Debian 10 with this tutorial. rsem is RNA-Seq by Expectation-Maximization

Introduction

In this tutorial we learn how to install rsem on Debian 10.

What is rsem

rsem is:

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute??s Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator.

There are three methods to install rsem on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install rsem Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install rsem

Install rsem Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install rsem

Install rsem 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 Debian. Update apt database with aptitude using the following command.

sudo aptitude update

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

sudo aptitude -y install rsem

How To Uninstall rsem on Debian 10

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

sudo apt-get remove rsem

Uninstall rsem And Its Dependencies

To uninstall rsem and its dependencies that are no longer needed by Debian 10, we can use the command below:

sudo apt-get -y autoremove rsem

Remove rsem Configurations and Data

To remove rsem configuration and data from Debian 10 we can use the following command:

sudo apt-get -y purge rsem

Remove rsem configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge rsem

Dependencies

rsem have the following dependencies:

References

Summary

In this tutorial we learn how to install rsem package on Debian 10 using different package management tools: apt, apt-get and aptitude.