ChIP-seq, RNA-seq and Hi-C: treatment, analysis and data visualization Présentiel

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

• 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