Introduction to RNA-seq data analysis

Course Description

This three-days bioinformatics training course provides an introduction to gene expression analysis by RNA sequencing (RNA-seq) technology. The course consists of lectures giving an overview of the individual steps in the RNA-seq data analysis pipeline and practical sessions using the external pageSushicall_made data analysis framework developed at FGCZ.

Learning Objectives

At the end of the course, the participants will:

• Understand the steps from raw reads to expression counts, differential expression and interpretation of gene lists using enrichment analysis
• Perform quality assessment of RNA-seq data, raw and processed
• Understand file formats commonly used in RNA-seq data analysis
• Gain an overview on common software tools for RNA-seq data analysis and their limitations
• Run RNA-seq pipeline to perform differential expression analysis using the FGCZ Sushi framework

Course Program

• Design NGS experiments for differential expression analysis
• Quality check of raw NGS data
• Align NGS reads against the reference genome
• Gene expression quantification 
• Differential expression analysis
• Gene set enrichment analysis (e.g., pathways, GO-categories)
• Applications of RNA sequencing and challenges

Important facts and how to apply

Language

The course will be entirely taught in English.

Participants

The course is limited to 12 participants only.

Target audience and prerequisites

Applicants should be FGCZ users that have NGS data generated or have data generation ongoing at the FGCZ. The practicals will be performed using the external pageSushicall_made framework, so no pre-existing knowledge of Unix or command line environment is required. Participants should bring their own laptop (only a few desktop computers are available for the ones who cannot bring a laptop).

Cost

Please refer to the main page of the bioinformatics courses.