STAR command not found

Introduction

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

STAR: command not found

or when using sudo you get the following error message

sudo: STAR: command not found

Solutions to STAR: command not found

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

In Ubuntu STAR is provided by rna-star package.

rna-star is:

Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, the authors experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy.

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

sudo apt-get -y install rna-star

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

You can also use apt command to install rna-star.

sudo apt -y install rna-star

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

sudo aptitude install rna-star

Summary

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