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

This course is now full with a long waiting list. We are no longer accepting applications. If you do not want to miss your chance to be part of the next session and remain informed about all training activities at SIB, we highly recommend you to keep an eye on our list of upcoming events and subscribe to our courses mailing list, if not yet done. Thank you for your understanding.

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 an introductory course on UNIX (eg UNIX fundamentals) 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: if you are on macOS / Linux, this is already the case; if you are on Windows, you should install a terminal which lets you do ssh (for instance mobaXterm).

Schedule

This course will be streamed.

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

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

Application

This course is over-subscribed with a very long waiting list. We are not accepting applications any more.

The registration fees for academics are 120 CHF and 600 CHF for for-profit companies.

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.

Deadline for free-of-charge cancellation is set to 19/08/2021. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

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.