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

Course Materials

• 09:30 - 10:00 Setup
• 10:00 - 12:30 Introduction to the Command Line (up to Writing Scripts and Working with Data)
• 12:30 - 13:30 LUNCH
• 13:30 - 14:30 Obtaining sequencing reads and assessing quality
• 14:30 - 17:00 Aligning sequencing data and counting

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Overview

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

Prerequisites

• No prior programming experience is required

Software

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

Instructors

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

Registration

Please use this link to register