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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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


For queries relating to collaborating with the Bioinformatics Core team on projects: bioinformatics-core@sheffield.ac.uk

Join our mailing list so as to be notified when we advertise talks and workshops by subscribing to this Google Group. You can also connect with us on Linkedin.

Requests for a Bioinformatics support clinic can be made via the Research Software Engineering (RSE) code clinic system. This is monitored by Bioinformatics Core staff, so we will ensure the appropriate expertise (which may involve individuals from multiple teams) will be available to help you

Queries regarding sequencing and library preparation provision at The University of Sheffield should be directed to the Multi-omics facility in SITraN or the Genomics Laboratory in Biosciences.