---
layout: page
organizer: Sheffield Bioinformatics Core
title: Introduction to the command line for Bioinformatics
excerpt: "Introduction to Unix"
startDate: 2023-01-16
endDate: 2023-01-16
startTime: 13.00
endTime: 17.00
city: Sheffield, or ONLINE
postcode: S3 7ND
country: United Kingdom
venue: Barber House Boardroom, Sheffield, or ONLINE
description: "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 will use a case study of dealing with next-generation sequencing data"
keywords: bioinformatics, bash, unix
difficulty: beginner
contact: bioinformatics-core@sheffield.ac.uk
---

- Sheffield - 16th January 2023
- 13:00 - 17:00pm
- Barber House Boardroom




## 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

- [crs.shef.ac.uk](https://crs.shef.ac.uk/) 

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

- [https://swcarpentry.github.io/shell-novice/](https://swcarpentry.github.io/shell-novice/)

## 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

- Mark Dunning, Bioinformatics Core Director
- Emily Chambers, Bioinformatics Core Analyst
- Lewis Quayle, Cancer Bioinformatician


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