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DESCRIPTION:## Overview\nThe recent advent of Nanopore direct RNA sequencin
 g allows for the first time to directly sequence full-length native RNA mo
 lecules without the need for retrotranscription or amplification. This new
  technology offers remarkable advantages compared to other sequencing meth
 ods\, 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. \nAt the sam
 e time\, the unique nature of Nanopore data poses various analytical chall
 enges\, thus requiring dedicated tools and new expertise. \nSince long rea
 d sequencing data QC and gene expression quantification is covered in the 
 [Long-read sequencing course](https://www.sib.swiss/training/course/202602
 26_LONGR)\, this course only shortly treats these aspects and focuses on m
 ore advanced and direct-RNA sequencing specific topics such as RNA modific
 ations detection\, isoform usage and polyA-tail analysis. \n\n\n## Audienc
 e\nThis course is designed for PhD students\, postdoctoral and other resea
 rchers in the life sciences from both academia and industry who are workin
 g with or are interested in working with direct-RNA sequencing data.\n\n##
  Learning outcomes\nAt the end of the course\, the participants are expect
 ed to be able to:\n\n- Choose a basecalling model that best fits their res
 earch question and basecall their raw data \n- Capture RNA modification si
 gnal indirectly through basecalling errors (in case of modifications for w
 hich no model is available) and directly through modkit\n- Extract per rea
 d information of isoform usage\, polyA tail length and RNA modification an
 d perform a quantitative analysis \n\n\n## Prerequisites\n##### Knowledge 
 / competencies\nYou should meet the learning outcomes of [UNIX Fundamental
 s](https://edu.sib.swiss/pluginfile.php/2878/mod_resource/content/4/cousel
 ab-html/content.html)\, and [Introduction to Bulk RNA-Seq: From Quality Co
 ntrol to Pathway Analysis](https://www.sib.swiss/training/course/20261008_
 IRNAS).\n\nIn case of doubt of your UNIX skills\, evaluate them with [this
  quiz](https://docs.google.com/forms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1F
 OaVYBbhBiaqcaHoBKNB27MQ/viewform?usp=sf_link) before registering.\n\nThis 
 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.\n\n##### 
 Technical\nYou are required to bring a laptop with a wifi connection. Soft
 ware installation instructions will be communicated before the course.\n\n
 ## Schedule \n\n### Day 1 ###\n- Introduction to direct RNA Nanopore seque
 ncing experiments\, data and software\n- RNA modification mapping based on
  basecalling errors with Epinano\n- RNA modification basecalling with modi
 fication-aware models and modkit\n\n### Day 2 ### \n\n- Single molecule re
 solution analysis: polyA tail length\, isoform usage\, per isoform RNA mod
 ification\n- Assignments in smaller groups: map RNA modifications in ribos
 omal RNA and in transcriptome \n\n\n## Application\n\nThe registration fee
 s for academics are **200 CHF** and **1000 CHF** for for-profit companies.
 \n\nYou will be informed by email of your registration confirmation. Upon 
 reception of the confirmation email\, participants will be asked to confir
 m attendance by paying the fees within 5 days.\n\nApplications close on 02
 /04/2026. Cancellation after this date will not be reimbursed. Please note
  that participation in SIB courses is subject to our [general conditions](
 https://www.sib.swiss/training/terms-and-conditions).\n\n## Venue and Time
 \nUniversity of Lausanne\, [Amphipôle building](https://planete.unil.ch/p
 lan/)\n\nThe course will start at 9:00 CET and end around 17:00 CET.\n\nPr
 ecise information will be provided to the registered participants in due t
 ime.\n\n## Additional information\nCoordination: Geert van Geest\n\n\nWe w
 ill recommend 0.5 ECTS credits for this course (given a passed exam at the
  end of the course).\n\n\nYou are welcome to register to the SIB courses m
 ailing list to be informed of all future courses and workshops\, as well a
 s all important deadlines using the form [here](https://lists.sib.swiss/ma
 ilman/listinfo/courses).\n\n\nPlease note that participation in SIB course
 s is subject to our [general conditions](http://www.sib.swiss/training/ter
 ms-and-conditions).\n\n\nSIB abides by the [ELIXIR Code of Conduct](https:
 //elixir-europe.org/events/code-of-conduct). Participants of SIB courses a
 re also required to abide by the same code.\n\n\nFor more information\, pl
 ease contact [training@sib.swiss](mailto://training@sib.swiss).
SUMMARY:Nanopore Direct RNA Sequencing Data Analysis
URL;VALUE=URI:https://www.sib.swiss/training/course/20260416_DIRNA
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