cuffcompare command not found

Introduction

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

cuffcompare: command not found

or when using sudo you get the following error message

sudo: cuffcompare: command not found

Solutions to cuffcompare: command not found

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

In Ubuntu cuffcompare is provided by cufflinks package.

cufflinks is:

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

This package provides the binary of cufflinks and associated tools, i.e. compress_gtf, cuffcompare, cuffdiff, cuffmerge, cuffnorm, cuffquant and gtf_to_sam.

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

sudo apt-get -y install cufflinks

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

You can also use apt command to install cufflinks.

sudo apt -y install cufflinks

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

sudo aptitude install cufflinks

Summary

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