Nanopore Direct RNA Sequencing Data Analysis

Overview

The recent advent of Nanopore direct RNA sequencing allows for the first time to directly sequence full-length native RNA molecules without the need for retrotranscription or amplification. This new technology offers remarkable advantages compared to other sequencing methods, for example it simplifies the accurate detection and quantification of mRNA isoforms, it allows the measurement of the polyA tail length and detection of RNA modifications at single molecule resolution. At the same time, the unique nature of Nanopore data poses various analytical challenges, thus requiring dedicated tools and new expertise. Since long read sequencing data QC and gene expression quantification is covered in the Long-read sequencing course, this course only shortly treats these aspects and focuses on more advanced and direct-RNA sequencing specific topics such as RNA modifications detection, isoform usage and polyA-tail analysis.

Audience

This course is designed for PhD students, postdoctoral and other researchers in the life sciences from both academia and industry who are working with or are interested in working with direct-RNA sequencing data.

Learning outcomes

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

• Choose a basecalling model that best fits their research question and basecall their raw data
• Capture RNA modification signal indirectly through basecalling errors (in case of modifications for which no model is available) and directly through modkit
• Extract per read information of isoform usage, polyA tail length and RNA modification and perform a quantitative analysis

Prerequisites

Knowledge / competencies

You should meet the learning outcomes of UNIX Fundamentals, and Introduction to Bulk RNA-Seq: From Quality Control to Pathway Analysis.

In case of doubt of your UNIX skills, evaluate them with this quiz before registering.

This course is intended for an audience of researchers with a certain degree of familiarity with RNA sequencing concepts. While not exclusively directed to attendees with bioinformatics training, the majority of the practicals will make use of command-line tools. Therefore a good level of experience with a *nix environment and the shell (e.g. Bash) are required.

Technical

You are required to bring a laptop with a wifi connection. Software installation instructions will be communicated before the course.

Schedule

Day 1

• Introduction to direct RNA Nanopore sequencing experiments, data and software
• RNA modification mapping based on basecalling errors with Epinano
• RNA modification basecalling with modification-aware models and modkit

Day 2

• Single molecule resolution analysis: polyA tail length, isoform usage, per isoform RNA modification
• Assignments in smaller groups: map RNA modifications in ribosomal RNA and in transcriptome

Application

The registration fees for academics are 200 CHF and 1000 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.

Applications close on [02/04/2026]. Deadline for free-of-charge cancellation is set to [02/04/2026]. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

University of Lausanne, Amphipôle building

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

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

Additional information

Coordination: Geert van Geest

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.