RNA-Seq: reads to differential genes and pathways
RNA sequencing (RNA-seq) is a common method used to understand the differences in gene expression and molecular pathways between two or more groups. This workshop introduces the fundamental concepts of RNA sequencing experiments and will allow you to try out the analysis using data from a study of Williams-Beuren Syndrome, a rare disease.
In the first part of the workshop you will learn how to convert sequence reads into analysis ready count data. To do this we will use nf-core/rnaseq – a portable, scalable, reproducible and publicly available workflow on Pawsey Nimbus Cloud. In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis!
Lead Trainers: Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub
Date/Time: 27 & 28 September 2022, 2-5pm AEST/1:30-4:30pm ACST/12-3pm AWST
This online workshop will take place over two three-hour sessions. You must attend both sessions in order 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.
By the end of the workshop you should be able to:
- List the steps involved in analysis of RNA-seq data
- Describe key concepts and considerations for RNA-seq experiments
- Describe the benefits of using nf-core workflows
- Deploy an RNA-seq nf-core workflow on Pawsey’s Nimbus Cloud to perform:
- Quality control
- Quantification to generate raw counts
- Use R/RStudio on Pawsey’s Nimbus Cloud to perform
- Quality control
- Identify differentially expressed genes using DESeq2
- Perform functional enrichment/pathway analysis
Who the workshop is for:
This workshop is for Australian researchers who have or will work on RNAseq data 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 webinar Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud in advance. You may join this webinar live on 20 September 2022. A recording will be posted on the Australian BioCommons YouTube Channel.
How to apply:
This workshop is free but participation is subject to application with selection.
Applications close at 11:59pm AEST, Sunday 11 September 2022.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). More information on the selection process is provided in our Advice on applying for Australian BioCommons workshops.
Successful applicants will be provided with a Zoom meeting link closer to the date.
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.