VALT_Summer_Course/index.md at master · ConesaLab/VALT_Summer_Course

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TrainingMaterial

VALT summer school - long-read transcriptomics

Valencia long-read transcriptomics summer school organized by LongTREC and the OSCARS project, a European Training Network on long-read transcriptomics. The course will cover the analysis of long-read RNA sequencing data, including technologies, experimental design, quality control, mapping, transcript identification and quantification, structural annotation evaluation, differential expression and haplotype analysis, and single-cell transcriptomics.

Academia/ Research Institution

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Organization	LongTREC	LongTREC	https://longtrec.eu/

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Organization	OSCARS	OSCARS	https://https://oscars-project.eu/

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Person	Ana Conesa

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Person	Carolina Monzó

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Person	Juan Francisco Servilla

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Person	Pablo Atienza

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Person	Nadja Nolte

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Person	Eamon McAndrew

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Person	Yalan Bi

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Person	Tian-Yuan Liu

https://creativecommons.org/licenses/by/4.0/

en-us

https://longtrec.github.io/summer_school/

Course Description

Welcome to the VALT Bioinformatics Summer School on the Analysis of Long-Reads Technology Data.

We have organized a comprehensive 3-day course designed for master's students, doctoral candidates, and early career postdoctoral fellows interested in exploring the exciting world of long-read RNA sequencing. Throughout this course, you will be introduced to a diverse range of topics — from fundamental technologies and basic data processing to advanced applications including long-read transcriptomics, single-cell analysis, and many other exciting topics.

Target Audience

This training is specifically designed for early career researchers who are:

In the grant application phase for long-read sequencing projects
Planning experimental design for studies centered around long-read technologies
Looking to expand their bioinformatics toolkit with cutting-edge long-read analysis methods

What Will You Learn?

Technologies & Fundamentals
- Comprehensive overview of different long-read sequencing technologies
- Best practices in experimental design
- Quality control evaluation using SQANTI-reads
Analysis & Applications
- Transcript identification and quantification using long-reads
- Structural annotation evaluation
- Differential expression analysis and haplotype identification
- RNA modifications detection with long-reads
Advanced Topics
- Single-cell and spatial transcriptomics approaches

Workshop Schedule

Day 1 | Foundation Day

Time	Session
09:00 - 12:30	Lecture: Different long-read sequencing technologies, experimental design, quality, mapping Lecturers: Carolina
12:30 - 13:30	Lunch Break
13:30 - 17:00	Hands-on: Different long-read mappers and QC evaluation with SQANTI-reads Lecturers: Tian

Day 2 | Transcript Analysis Day

Time	Session
09:00 - 12:30	Lecture & Hands-on: Transcript identification and quantification using long reads Lecturers: Yalan and Ana
12:30 - 13:30	Lunch Break
13:30 - 17:00	Lecture & Hands-on: Evaluation of structural annotation using long reads RNA sequences Lecturers: Pablo

Day 3 | Advanced Analysis Day

Time	Session
09:00 - 12:30	Lecture & Hands-on: Differential expression and haplotype analysis using long reads Lecturers: Nadja
12:30 - 13:30	Lunch Break
13:30 - 17:00	Lecture & Hands-on: Single-cell transcriptomics with long reads Lecturers: Eamon and Fran