RNA sequencing (RNAseq) is a popular and powerful technique used to understand the activity of genes. Using differential gene profiling methods, we can use RNAseq data to gain valuable insights into gene activity and identify variability in gene expression between samples to understand the molecular pathways underpinning many different traits.

In this hands-on workshop, you will learn RNAseq fundamentals as you process, analyse, and interpret the results from a real RNAseq experiment on the command-line. In session one, you will convert raw sequence reads to analysis-ready count data with the nf-core/rnaseq workflow. In session two, you’ll work interactively in RStudio to identify differentially expressed genes,perform functional enrichment analysis, and visualise and interpret your results using popular and best practice R packages.

This workshop is being delivered as a part of the Australian BioCommons Bring Your Own Data Platforms Project and will provide you with an opportunity to explore services and infrastructure built specifically for life scientists working at the command line. By the end of the workshop, you will be familiar with Pawsey’s Nimbus cloud platform and be able to process your own RNAseq datasets and perform differential expression analysis on the command-line.

Lead Trainers:

Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub
Dr Georgina Samaha, Bioinformatics Group Lead, Sydney Informatics Hub

Date/Time: 11 & 12 October 2023, 2 - 5pm AEST/1:30 - 4:30pm ACST/12 - 3pm AWST

Location: Online

Format:

This online workshop will take place over two three-hour sessions. You must attend both sessions to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action.

Learning outcomes:

By the end of the workshop you should be able to:

• List the steps involved in RNAseq data processing and differential expression analysis
• Understand key concepts and considerations for RNAseq experiments
• Describe the benefits of using nf-core workflows
• Run the nf-core/rnaseq workflow to perform:
  • Quality control
  • Read alignment
  • Read quantification to generate raw counts
• Use R/RStudio on to perform:
  • Quality control
  • Identify differentially expressed genes
  • Perform functional enrichment/pathway analysis

Who the workshop is for:

This workshop is for Australian researchers or bioinformaticians who are new to working with RNAseq datasets on the command-line interface and have or will be using bulk RNAseq datasets to identify differentially expressed genes as part of their projects. You must be associated with an Australian organisation for your application to be considered.

The workshop will be conducted in a Unix environment and will use R/RStudio.

Basic command line knowledge is required. You must know how to navigate the directory structure and copy files between the computers. If you need a refresher on Unix/Linux try this online tutorial.

Basic knowledge of R/RStudio is required. You must know how to set up directories, run commands, reading in and outputting files. If you need a refresher on R/RStudio try the Introduction to R and RStudio section of this online tutorial.

It’s recommended that you watch the following webinars before joining the workshop:

• Getting started with RNAseq: Transforming raw reads into biological insights
• Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud.

How to apply:

Apply here

This workshop is free but participation is subject to application with selection.

Applications close at 11:59pm AEST, Monday 25 September 2023.

Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date.

More information on the selection process is provided in our Advice on applying for Australian BioCommons workshops.

Apply here

This workshop is presented by the Australian BioCommons, Sydney Informatics Hub and Pawsey Supercomputing Research Centre with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.

This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to Australian BioCommons.