Introduction to the command line for Bioinformatics

  • Sheffield - 26th June 2023
  • 19:30 - 16:30pm

  • The Diamond - Workroom 1

  • Registration Link

Overview

This course offers an introduction to working with Linux for Bioinformatics. 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 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
  • 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 -Write short scripts to document an analysis

Aims:- During this course you will learn about:

  • Quality assessment of NGS data
  • A basic workflow for processing RNA-seq data
  • Workflow management systems; such as nextflow

Prerequisites

  • No prior programming experience is required

Software

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

Unix Reference Sheet

Feel free to download this “cheat sheet” describing some of the commands that we will be covering

Schedule (Provisional)

Instructors

  • Mark Dunning, Bioinformatics Core Director
  • Emily Chambers, Bioinformatics Core Analyst
  • Ben Draper, PhD Student, CBE
  • Jack Riley, PhD Student, Biosciences

Feedback

Please use this form to give us some feedback on the workshop


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.