Introduction to the analysis of bulk RNA-seq data for prediction of differentially expressed genes, May 28, 2025, 10:00-17:00

by Andre Gohr (SciComp@CBG), Erdi Kücük (SciComp@CBG)

Wednesday 28 May 2025, 10:00 → 17:00 Europe/Berlin

Seminar room, ground floor (CSBD)

Contents: You will learn theory of RNA-seq data crucial for analysing bulk RNA-seq for prediction of differentially expressed genes. Knowledge will be strengthend by performing an example analysis of public RNA-seq data yourself. Topics covered include:

1. Types of sequencing approaches
2. Important data and file types of NGS data
3. Library prep and types of sequencing reads
4. Quality control
5. Read trimming
6. Read mapping
7. Getting counts of mapped reads per gene
8. Statistical analysis of read counts per gene for the prediction of differentially expressed genes
9. Analysis and visualization of predictions

Schedule:

1. 10:00-10:15: Welcome
2. 10:15-12:00: Lecture by Erdi on the theoretical background of RNA-seq data relevant for the practical analysis
3. 12:00-13:00: Lunch break
4. 13:00-17:00 Live coding with Andre ie. participants by themselves on their laptops follow and do a guided step-by-step analysis of public RNA-seq data with Galaxy

 

Target audience: This course is ideal for anyone curious about RNA-seq data analysis and who might want to explore or reanalyze public or in-house RNA-seq datasets from time to time.

Capacity:

1. 15 places for CBG members
2. We need to select participants if more than 15 persons apply

Requirements:

1. Have a CBG affiliation
2. Having completed the questionnaire during application
3. Bring your own laptop with a recent web browser installed

Not required:

1. Programming
2. Firm with Linux / Mac
3. Firm in working with the terminal / bash
4. Experience with NGS data
5. Experience with the bioinformatics analysis of NGS data
6. Own RNA-seq data to be analyzed

Further reading:

1. 10 min video on YouTube with broad overview on NGS
2. Paper 2018: Overview of next generation sequencing technologies
3. Paper 2021: Next-generation sequencing technologies: An overview
4. Paper 2023: Next-generation sequencing technology: Trends and Advancements
5. Galaxy training material
6. Our live coding builds upon this original self-study Galaxy training on reference-based RNA-seq data analysis
7. Current protocols 2024: RNA-Seq Data Analysis: A Practical Guide for Model and Non-Model Organisms
8. RNA-seqlopedia by the Cresko Lab

Live_coding_data data.zip