ChIP-seq, RNA-seq and Hi-C: treatment, analysis and data visualization Présentiel
Dernière mise à jour : 12/02/2026
Unité de recherche
Description
Day 1: ChIP-seq and RNA-seq data pre-processing
- Initiation to Linux command lines (3 h)
- Basic notions of ChIP-seq, RNA-seq and Hi-C and their analysis pipeline, principle of spike-in normalization
- Pre-treatment of data (quality of raw data, alignments, sequencing artifacts)
- Exploration of aligned data (fragments size estimation, alignment quality)
Days 2 and 3: ChIP-seq analysis
- Generation of signal files (.wig) using the R-PASHA package
- Visualization of .wig files and isolation of enriched regions adapting detection parameters (MACS2 or using a genome browser option)
- Initiation to meta-profiling around regions of interest (genes, TSS, TES, enhancers)
- Enrichment of functional annotations (gene ontology)
- Motif search in enriched regions
- External spike-in normalization
Day 4: RNA-seq analysis
- Quantification of gene expression in RNA-seq data (RPKM)
- Spike-in normalization principle
- Differential gene expression analysis for transcripts and exons
Day 5: Hi-C analysis
- Quality controls, alignment and filtering of Hi-C data
- Generation of a chromosomal interaction map
- Visualization and interpretation of the interaction matrix
- Identification of subnuclear compartments
- Identification of Topologically Associating Domains (TADs) and loops
- Presentation of few databases and visualization tools for Hi-C
- Discussion (1 h) around participants questions and own problematics
Objectifs de la formation
- Learn how to plan a simple experiment of ChIP-seq or RNA-seq
- Acquire the skills to evaluate data quality for transcriptome and gene regulation experiments
- Understand and apply the principal methods and analysis tools for RNA-seq and ChIP-seq
- Be able to visualize data in a genome browser and extract enriched regions
- Learn how to manipulate and annotate enriched regions files using bedtools
- Become acquainted with the principal methods of analysis for long-distance genomic interactions (Hi-C) and generate chromosomal interaction maps
Public visé
Engineers and researchers in biology
Prérequis
Knowledge of basic command lines under Linux can be useful but not mandatory. A recall of basic knowledge will be proposed.
Modalités pédagogiques
Lectures (5h) and practical courses (27h) supervised by 1 teacher for 4 attendees.
Moyens et supports pédagogiques
Paper support, files in PDF format and a Linux virtual machine will be made available to the trainee.
Modalités d'évaluation et de suivi
Ongoing formative assessments throughout the course. A certificate of cmpletion is issued at the end of the training
Formateurs
Informations sur l'admission
Admission to this training programme is not subject to any examination, test or prior selection; registration is confirmed upon receipt of a complete application file and validation by the training provider.
Modalités tarifaires spécifiques
All our training courses are VAT exempt. Enjoy exclusive volume discounts: save 5% when registering 3-4 participants, 10% for 5-6, and 20% for groups of 7 or more. CNRS employees benefit from a special 20% discount.
Informations sur l'accessibilité
Our organisation is committed to ensuring inclusive and equitable access to its training programmes, whether delivered online or in person, for all participants, including people with disabilities. A dedicated accessibility contact is available to assess individual needs and, where possible, implement appropriate pedagogical, technical and organisational adjustments