Analytics 2: Introduction to the command-line for Bioinformatics, Mar 2022

Course content

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.

Who is this for?

This is mandatory training for second years i.e. students who started in 2020, and follows on from the Analytics R1 undertaken in the first year. This is for all DTP students, including core DTP students plus iCASE and White Rose Network students.


No prior programming experience is required. Computers will be provided. You can bring your own laptop to the workshop if you wish but it will need a working wi-fi connection and you will have to let the tutor know in advance so a temporary York password can be created for you.

Learning outcomes

After this course you should be able to:

  • Connect to a Unix / Linux system
  • Navigate around a file system by issuing commands; rather than using a Desktop environment
  • Move and copy files and directories within the Linux system
  • Work with text files
  • Run programs from the command-line
  • Run quality assessment tools on data derived from High-throughput sequencing experiments
  • Align sequencing reads against a reference genome

When and where

This course will be held in-person on Thursday 24th March 2022 at The University of York. Transport will be provided for Leeds and Sheffield students. Please note that Leeds and Sheffield students will have to get up very early that morning so you do not miss the coaches! Transport details will be issued nearer the time.


Click the links for an insight into what will be covered in each module.

09:30 Arrive

10:00 – 10:30 Course Setup

10:30 – 12:45 Introduction to the command line

13:30 – 14:30 Obtaining sequencing data and assessing quality

14:30 – 16:00 Aligning sequencing data and quantification


The course will be delivered by Mark Dunning of The University of Sheffield.


Lunchtime refreshments will be provided.

Travel arrangements

Details of coach travel for Leeds and Sheffield students will be issued with detailed joining instructions via email. Please note that you will have to get up very early that morning so you do not miss the coaches! Please note that if you choose not to use the coaches provided, you will not be able to claim your travel costs. Car parking on the York campus is in very limited supply and is on a first-come, first-served basis so there is no guarantee of a space.

Analytics R1 and Analytics R2 are running concurrently on the same day therefore both year groups will travel together.

Covid regulations

Following the Government announcement on Monday 21 February, which set out the plan for ‘living with Covid’, The University of York has updated its guidance to staff and students:

  • We’re asking our community to continue to protect others by staying at home if you feel unwell, wearing a face covering and getting booster vaccinations.
  • Participants should do a lateral flow test before attending the Analytics course. If it is positive, please stay at home and alert the DTP Co-ordinator that you will not be attending. (Catherine Liddle, email:
  • Any changes to these measures will be advised prior to the course date

How to register

Registration closes on Friday 18th February 2022. Please use the following link:


If you have any queries or you feel you already have sufficient previous experience of a particular module, please discuss this directly with the tutor, Mark Dunning, email:

For general DTP queries, contact Catherine Liddle, White Rose BBSRC Doctoral Training Partnership Co-ordinator, e-mail: