Overview

This three-day course will provide an overview of the RNA-seq analysis pipeline, as well as the downstream analysis of the resulting data using bioconductor packages in R. The course will cover the following topics:

The structure of an RNAseq analysis pipeline:

Raw data quality check;
RNAseq reads alignment;
Gene Expression level quantification and normalization by reads counting;
De novo Transcripts reconstruction and differential splicing.

Overview of downstream analysis

Differential Expression analysis with R/Bioconductor packages;
Class discovery: usage of Principal Component Analysis, Clustering, Heatmaps, Gene Set Enrichment Analysis in RNA-seq analysis.

Next Generation Sequencing (NGS) techniques will not be covered in this course; experimental design as well as the statistical methods will not be detailed in this course.

Audience

Life scientists who are new in the RNA-seq data field but have some R and statistical knowledge.
Prerequisites
Knowledge / competencies

Participants should already have a basic knowledge of Next Generation Sequencing (NGS) techniques; this course will discuss only the data analysis steps and not the data generation.
A basic knowledge in statistics is required. Participants should know about p-values, student T-test, multiple testing correction and classification, PCA.
A basic knowledge of R is also required. Participants should know how to read files, run PCA, do classification, visualise heatmaps using R command lines.
A basis knowledge of Unix is also required.

Technical

A Wi-Fi enabled laptop with the latest version of R and Bioconductor installed. Participants with windows machines should have enabled WLS2, so they can run linux software

Learning objectives

At the end of the course, participants will be able to:

run a RNA-seq pipeline on a small dataset composed of two groups;

describe an RNA-seq experimental design;

describe pseudo-alignments and alignment software;

estimate data quality;

normalise counts;

know and understand the essential steps of a simple gene expression analysis issued from RNA sequencing;

manipulate gene expression matrices and differential expression tables;

perform a differential expression analysis based on R/Bioconductor packages (DeSeq2, ...).

Schedule

DAY1
9:00 - 10:30 - Introduction to RNA sequencing 10:30 - 10:45 - Coffee Break 10:45 - 12:30 - RNAseq analysis pipeline, part I 12:30 - 13:30 - Lunch Break 13:30 - 15:00 - RNAseq analysis pipeline, part II 15:00 - 15:15 - Coffee break 15:15 - 17:00 - Practicals

DAY2 9:00 - 10:30 - Differential Expression analysis 10:30 - 10:45 - Coffee Break 10:45 - 12:30 - Differential splicing 12:30 - 13:30 - Lunch Break 13:30 - 15:00 - Practicals 15:00 - 15:15 - Coffee break 15:15 - 17:00 – Practicals

DAY3 9:00 - 10:30 - Differential Expression analysis with DESEQ2 10:30 - 10:45 - Coffee Break 10:45 - 12:30 - Downstream analysis 12:30 - 13:30 - Lunch Break 13:30 - 15:00 - Practicals 15:00 - 15:15 - Coffee break 15:15 - 17:00 - Practicals

Application

Registration fees are 180 CHF for academics and 900 CHF for for-profit companies.
You will be informed by email of your registration confirmation, and you will be asked to complete the payment of the registration fees within 5 days.
Deadline for registration and free-of-charge cancellation is set to 24/04/2023. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to this and other general conditions, available here.

Venue and Time

This course will only be streamed online.

It will start at 9:00 CET and end around 17:00 CET.

Precise information will be provided to the participants before the course.

Additional information

Coordination: Valeria Di Cola, SIB Training Group.
We will recommend 0.75 ECTS credits for this course (given a passed exam at the end of the course).
You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.
Please note that participation in SIB courses is subject to our general conditions.
SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.
For more information, please contact training@sib.swiss.