stringtie command not found

Introduction

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

stringtie: command not found

or when using sudo you get the following error message

sudo: stringtie: command not found

Solutions to stringtie: command not found

How To Fix stringtie: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu stringtie is provided by stringtie package.

stringtie is:

The abundance of transcripts in a human tissue sample can be determined by RNA sequencing. The exact sequence sampled may be random, depending on the technology used. And it may be short, i.e. shorter than the transcript. At some point, many shorter reads need to be assembled to the model the complete transcripts.

StringTie knows how to assemble of RNA-Seq into potential transcripts without the need of a reference genome and provides a quantification also of the splice variants.

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

sudo apt-get -y install stringtie

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

You can also use apt command to install stringtie.

sudo apt -y install stringtie

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

sudo aptitude install stringtie

Summary

In this tutorial we learn how to fix stringtie command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.