Welcome to the LongTREC Bioinformatics Summer School on Analysis of Long-Reads Technology Data.
We have organized a comprehensive 4-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.
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Technologies & Fundamentals
- Comprehensive overview of different long-read sequencing technologies
- Best practices in experimental design
- Quality control evaluation using SQANTI-reads
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Analysis & Applications
- Transcript identification and quantification using long reads
- Structural annotation evaluation
- Differential expression analysis and haplotype identification
- RNA modifications detection with long reads
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Advanced Topics
- Single-cell transcriptomics approaches
- Principles and practical applications of metatranscriptomics
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
- Required Skills: Familiarity with command line interfaces
- Participants should be comfortable with basic Unix shell commands as taught in the Software Carpentry lesson on The Unix Shell
- We recommend working through these materials before the training if you need to refresh your skills
| Time | Session |
|---|---|
| 09:00 - 12:30 | Lecture: Different long-read sequencing technologies, experimental design, quality, mapping Lecturers: Carol, Satrio, Sami and Tian |
| 12:30 - 13:30 | Lunch Break |
| 13:30 - 17:00 | Hands-on: Different long-read mappers and QC evaluation with SQANTI-reads Lecturers: Sami and Tian |
| Time | Session |
|---|---|
| 09:00 - 12:30 | Lecture & Hands-on: Transcript identification and quantification using long reads Lecturers: Fabio, Ana, Fabian and Yalan |
| 12:30 - 13:30 | Lunch Break |
| 13:30 - 17:00 | Lecture & Hands-on: Evaluation of structural annotation using long reads RNA sequences Lecturers: Fabio, Ana, Fabian and Yalan |
| 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: RNA modifications with long reads Lecturers: Leda |
| Time | Session |
|---|---|
| 09:00 - 12:30 | Lecture & Hands-on: Single-cell transcriptomics with long reads Lecturers: Eamon and Fran |
| 12:30 - 13:30 | Lunch Break |
| 13:30 - 17:00 | Lecture & Hands-on: Metatranscriptomics with long reads Lecturers: Carmen |
We thank Pedro Fernandes for providing this template and his training session to prepare this course:
https://www.linkedin.com/in/pedrofernandesbioinformatics/
https://orcid.org/0000-0003-2124-0241
pmlfern@gmail.com