Introduction to RNA-Seq Analysis

Dates

Tuesday November 12th 2024 13:00 - 16:00

Online, and Pam Liversidge Building E06, - University of Sheffield

Registration

University of Sheffield staff / students are recommended to book via myDevelopment

Otherwise, please use this link to register for the course. There are options for attending online and in-person.

Course Materials

Overview

The workshop will be hands-on; working through exercises and watching demonstrations from the lecturers.

High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. We will describe the steps involved to go from a count matrix to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Degust interface (https://degust.erc.monash.edu/) to demonstrate tasks such as quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis

Please note that the course will not cover the analysis of RNA-seq data using the R programming langugage. We will also not explicitly cover the alignment of RNA-seq sequences against a reference genome

Who should attend this course?

Researchers in life sciences who want to get an appreciation for the computational steps involved in RNA-seq analysis, but not neccesarily wishing to execute the pipeline for themselves.

Objectives:- After this course you should be able to:

  • Appreciate some of the issues that can arise when designing an RNA-seq experiment
  • Interpret an Multi-dimensional scaling (MDS) plot to check for batch effects and confounding factors
  • Use Degust to generate a statistically robust gene list
  • Perform a gene set enrichment analysis using available online tools

Aims:- During this course you will learn about:

  • Basic principles of Experimental design for RNA-seq experiments
  • The steps in a best-practice pipeline for RNA-seq analysis
  • Configuring the Degust interface to perform different types of differential expression
  • The theory behind popular methods for pathways and gene set enrichment analysis

Instructors


For queries relating to collaborating with the Bioinformatics Core team on projects: bioinformatics-core@sheffield.ac.uk

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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.