rsem-generate-data-matrix command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

rsem-generate-data-matrix: command not found

or when using sudo you get the following error message

sudo: rsem-generate-data-matrix: command not found

Solutions to rsem-generate-data-matrix: command not found

How To Fix rsem-generate-data-matrix: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu rsem-generate-data-matrix is provided by rsem package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install rsem

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install rsem.

sudo apt -y install rsem

Or if you have aptitude installed you can use the following command.

sudo aptitude install rsem

Summary

In this tutorial we learn how to fix rsem-generate-data-matrix command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.