VALT summer school long-read transcriptomics
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: Ana Conesa |
| 12:30 - 13:30 | Lunch Break |
| 13:30 - 17:00 | Hands-on: Different long-read mappers and QC evaluation with SQANTI-reads Lecturers: Carol and 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 and Pablo |
| 12:30 - 13:30 | Lunch Break |
| 13:30 - 17:00 | Lecture & Hands-on: Single-cell transcriptomics with long reads Lecturers: Eamon and Fran |
Instructors
The source for this course webpage is in github.
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