Introduction to the command line for Bioinformatics

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

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.

Some prior knowledge of working with the command-line is required. Those based in Sheffield can sign-up for an introductory course from the Research-IT team at this link

In particular the Introduction to Linux course should be attended, and optionally Linux Shell Scripting Tutorial and Introduction to Running Software on HPC would be beneficial

Those outside Sheffield and interested in attending are recommended to follow these lessons from Software Carpentry

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:

  • Run Bioinformatics programs from the command-line
  • Locate and download genome references from resources such as Ensembl
  • Perform QC on a set of sequencing reads
  • Use salmon to produce gene quantifications

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

Instructors

  • Dr. Mark Dunning, Bioinformatics Core Director
  • Dr. Akshay Bhat, Bioinformatics Core Analyst

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.