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Objectifs

After this course, you should:
• know the main next generation sequencing applications and their specificities
• know the main library preparation protocols, their advantages and biases
• know relevant considerations for experimental design of RNA-seq or ChIP-seq experiments
• know the main file formats generated by an Illumina sequencer and used by the main software dedicated to next generation sequencing data analysis
• understand methodologies for RNA-seq and ChIP-seq data analysis : from raw data analysis to data interpretation and visualization
• know the main functionalities of Galaxy
• know the main functionalities of a genome browser

Pré-requis

Aucun

Public

Biologists who are applying or planning to apply high throughput sequencing technologies in their research

Programme

• 2nd generation sequencing technologies and introduction to the 3rd generation technologies (talk)
• Library preparation methodologies for DNA (re)sequencing (talk)
• Genome browsers and associated mining tools (talk + hands-on)
• Library preparation methodologies for RNA-seq (talk)
• Primary analysis of next generation sequencing data : main file formats (FASTQ, SAM/BAM, WIG, BED…) and quality controls (talk + hands-on)
• Next generation sequencing read mapping (talk)
• RNA-seq data analysis: quantification, normalization and statistical analysis (talk), functional analysis, visualization and data interpretation (hands-on)
• Introduction to Galaxy (hands-on)
• Library preparation methodologies for ChIP-seq (talk)
• ChIP-seq data analysis: data visualization, peak detection and annotation, clustering and motif analysis (talk + hands-on)
• Integration of RNA-seq and ChIP-seq data (hands-on)

Durée

2 days

Intervenants

Céline KEIME et Stéphanie LE GRAS (IGBMC)

Dates

29 and 30 September 2016

Lieu

Cronenbourg campus, 23 rue du Loess, Strasbourg

Informations

Ressources humaines > Pôle formation
Mme Gabrielle BOULANGER
formation@alsace.cnrs.fr