RNA-seq course - international course for the programme COURSES@CRG¶
16-20 March 2026
Decoding Transcriptomes: A Practical Course on RNA-seq¶
https://courses.crg.eu/events/decoding-transcriptomes-practical-course-rna-seq
This hands-on program provides a comprehensive introduction to RNA sequencing, guiding participants through the complete workflow from sample preparation to data analysis. Participants will gain practical experience in RNA quality control, mRNA library preparation for Next Generation Sequencing (NGS), and library quality control. On the computational side, they will work with real sequencing data to learn key steps including data quality assessment, alignment, quantification, differential expression analysis, and functional interpretation.
The course integrates laboratory practice with computational training, equipping participants with the skills needed to design robust RNA-seq experiments and to apply reproducible analysis workflows following the FAIR practices. The program is complemented by theoretical lectures on state-of-the-art transcriptomics and bioinformatics, a guided visit to the CRG Genomics Unit, and networking activities.
This repository covers only the computational part of the course.
The webpage is at https://biocorecrg.github.io/RNAseq_coursesCRG_2026/
Agenda¶
Day 3 - Wed 18 March 2026¶
11:30 - 12:00 Talk: Pre-processing of raw data and fastq format - What happens with data after the libraries were sequenced (Anna Delgado)
12:00 - 12:30 Talk: FAIR & Reproducible practices in Bioinformatics - containers, public repos, git/GitHub (Toni Hermoso)
12:30 - 13:00 Talk: RNA-seq data analysis: Workflow & Approaches (Luca Cozzuto) here or later to cover: Map reads to genome or transcriptome? Existing approaches/methods to read mapping in an RNA-seq experiment: pros and cons, which to choose?
13:00 - 14:00 Lunch
14:00 - 14:30 Hands-on: Basics of Linux CLI (Toni Hermoso)
14:30 - 16:00 Hands-on: Read QC: fastq format, FastQC, FastqScreen, kraken, MultiQC (Anna)
16:00 - 16:15 Coffee break
16:15 - 17:00 Hands-on: Read pre-processing: adapter trimming, riboPicker, MultiQC (Luca)
17:00 - 18:00 Hands-on: Getting reference genome/transcriptome and annotation (ENSEMBL, Gencode, UCSC Genome Browser), GTF/GFF format (Luca)
Day 4 - Thu 19 March 2026¶
9:00 - 11:00 Hands-on: Read mapping to the reference genome/transcriptome and quantification (STAR, Salmon, SAM/BAM format, samtools, explore BAM/bigwig file in the UCSB Genome Browser, gene/transcript quantification, QualiMap) (Luca)
11:00 - 11:30 Coffee break
11:30 - 13:00 Hands-on: Review R basics (RStudio) (Sarah Bonnin)
13:00 - 14:00 Lunch
14:00 - 16:00 Hands-on: DESeq2: import data from STAR and SALMON, filtering and normalization (vst, log2(deseq-native)), PCA, sample clustering, boxplots for selected genes, batch correction using ComBat (for that we will need to use a different dataset) (Fabian)
16:00 - 16:15 Coffee break
16:15 - 18:00 Hands-on: DE analysis using DESeq2. Gene selection, volcano plots, heatmaps. Functional analysis using R packages (for gene sets) and the GSEA application (for all genes) (Fabian)
18:00 - 21:00 Social activity
Day 5 - Fri 20 March 2026¶
9:00 - 11:00 Hands-on: Running the full analysis using an nf-core pipeline (Luca)
11:00 - 11:30 Coffee break
11:30 - 12:00 Talk: Design of RNA-seq experiment & Beyond bulk RNA-seq (Julia)
12:00 - 13:00 Q&A and General discussion
13:00 - 14:00 Lunch