Introduction to the command line for Bioinformatics

  • Sheffield - 12th February 2020
  • 09:30am - 5pm
  • Bartolome House, Seminar Room EG03

Course Materials


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This course offers an introduction to working with Linux. We will describe the Linux environment so that participants can start to utilize command-line tools and feel comfortable using a text-based way of interacting with a computer. We give example of processing data arising from Next-Generation Sequencing experiments, in particular an RNA-seq experiment.

This course is highly-recommended as a pre-requisite for our course RNA-seq Analysis in R

Who should attend this course?

Those wanting to use the command-line to perform data analysis; particularly those with next-generation sequencing data such as RNA-Seq

Objectives:- After this course you should be able to:

  • Connect to a Unix / Linux system
  • Manipulate files and directories within the Linux system
  • Work with text files
  • Understand how to structure and write a simple shell script
  • Run programs from the command-line

Aims:- During this course you will learn about:

  • Navigating through a Unix file system
  • Creating and deleting files
  • Searching for files and for text within a file
  • Writing and executing simple shell scripts


  • No prior programming experience is required


  • No software is required. You will be given access to an AWS machine on the day


  • Mark Dunning, Bioinformatics Core Director
  • Katjusa Koler, PhD Student
  • Emily Chambers, Bioinformatics Core Analyst
  • Sokratis Kariotis, PhD Student


Please use this link to register