Introduction to bulk RNA-Seq: From Quality Control to Pathway Analysis

Overview

This two-day course will present the theory and bioinformatics tools required to analyze RNA-seq gene expression data. The course will present the theory and bioinformatics tools required to analyse RNA-seq gene expression data, from the raw data until the biological interpretation. The following topics will be discussed:

• Quality control
• Mapping to genomes & transcriptomes
• Read counting, gene & exons differential expression analysis
• GO enrichment and pathway analysis

Audience

This course is addressed to life scientists or bioinformaticians familiar with "Next Generation Sequencing" who wish to acquire the necessary skills to analyse RNA-seq gene expression data.

Learning outcomes

At the end of the course, the participants are expected to:

• Describe advantages and pitfalls of RNA sequencing
• Design their own experiment
• Perform the downstream analysis using command line software (QC, mapping, counting, differential expression analysis, pathway analysis, etc)
• Critically assess the quality of their results at each step of the downstream analysis

Prerequisites

Knowledge / competencies

Participants should already have a basic knowledge in Next Generation Sequencing (NGS) techniques.

Basic knowledge of the R statistical software and completion of the UNIX fundamentals e-learning module or equivalent knowledge is also required.

Technical

You are required to have your own Wi-Fi enabled laptop.

You should also have access to a terminal on your computer:

• macOS / Linux: you can use the default terminal. If you are unfamiliar with scp, you may want to install a graphical client for file transfer, such as fileZilla
• Windows, you should install a terminal which lets you do ssh (for instance mobaXterm).

Schedule

This course will be held ONLY in person at the University of Basel. It will start at 9:00 and end around 17:00.

Precise information will be provided to the participants in due time.

Application

The registration fees for academics are 200 CHF and 1000 CHF for for-profit companies.
While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

Applications will close as soon as the places will be filled up. Deadline for free-of-charge cancellation is set to 12/09/2025. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Additional information

Coordination: Monique Zahn, SIB Training Group.

We will recommend 0.5 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.