An introduction to Nanopore direct RNA Sequencing

Dates

18-22 January 2021

Due to the COVID-19 outbreak, this course will be held online

 

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 short-read sequencing methods, for example it greatly simplifies the accurate detection and quantification of RNA isoforms, it allows the measurement of the polyA tail length and also allows the detection of RNA modifications. At the same time, the unique nature of Nanopore data poses various analytical challenges, thus requiring dedicated tools and new expertise.

 

This course is structured over 5 days of theoretical and hands-on training and covers the majority of the concepts and challenges commonly faced when analysing direct RNA-Seq data. It will start from common tasks such as data QC and gene expression quantification and then move on to more advanced topics such as transcriptome assembly, polyA-tail length measurements and RNA modifications detection.

 

 

Target audience and assumed background

 

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 some experience with a Unix environment (e.g. Linux or MacOS) and the shell (e.g. Bash) are highly desirable. Some familiarity with R will also be an advantage.

 

 

Program


Monday - Classes from 2 to 8 pm Berlin time.

 

Theoretical introduction to Nanopore direct RNA-Sequencing and its applications

 

 

This first session will introduce the course and provide various concepts related to the execution and analysis of direct RNA-Seq experiments:

 

* Nanopore sequencing in general: what it is and how it works

 

* Application of Nanopore sequencing: DNA, cDNA and direct RNA (dRNA-Seq)

 

* Advantages and disadvantages of dRNA-Seq: comparison with Sequencing by Synthesis

 

* Direct RNA-Seq chemistry

 

* Format and structure of Nanopore data (fast5 files, etc.)

 

* From signal to sequence: the basecalling process

 

* Bioinformatics ecosystem for Nanopore: an introduction

 

* Advanced applications (e.g. targeted sequencing, metabolic labelling)

 

Instructors

 

Dr. Tommaso Leonardi

 

 

 

 

 

COst overview

Package 1

 

 

 

  480 €


Cancellation Policy:

 

 

 

> 30  days before the start date = 30% cancellation fee

 

< 30 days before the start date= No Refund.

 

 

 

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.