htseq-count-barcodes command not found

In this troubleshooting guide we learn how to fix htseq-count-barcodes command not found error message

Introduction

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

htseq-count-barcodes: command not found

or when using sudo you get the following error message

sudo: htseq-count-barcodes: command not found

In Ubuntu htseq-count-barcodes is provided by python3-htseq package.

python3-htseq is:

HTSeq can be used to performing a number of common analysis tasks when working with high-throughput genome sequencing reads:

Getting statistical summaries about the base-call quality scores to study the data quality.
Calculating a coverage vector and exporting it for visualization in a genome browser.
Reading in annotation data from a GFF file.
Assigning aligned reads from an RNA-Seq experiments to exons and genes.

This package contains the Python 3 module.

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

sudo apt-get -y install python3-htseq

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

You can also use apt command to install python3-htseq.

sudo apt -y install python3-htseq

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

sudo aptitude install python3-htseq

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