Biostatistical and bioinformatic analysis of RNA Seq Andréa Rau and Jordi

Biostatistical and bioinformatic analysis of rna seq

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Biostatistical and bioinformatic analysis of RNA-Seq : Andréa Rau and Jordi Estellé Introduction to differential analysis of RNA sequencing data Normalization of RNA-seq data: technical biases due to library size and GC content Statistical analysis to identify differentially expressed genes from RNA sequencing data: models and tests for differential expression in unreplicated and replicated data, correction for multiple testing Gene ontology enrichment analysis for RNA-seq data Afternoon : 14:00-18:00 Andréa Rau and Jordi Estellé Practice: transcriptome analysis with RNA-Seq data (from raw data to functional analysis) Differential analysis of Illumina RNA-seq data from humans using the DESeq Bioconductor package 16:00-16:30 Coffee break 16:30-18:00 Practice (continued)
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Friday, October 26 Morning: 8:30-13:00 8:30:10:30 NGS for genome polymorphism analysis: Jordi Estellé 10:30-11:00 Coffee break 11:00-13:00 Practice: read mapping and variant calling Jordi Estellé and Purnima Pachori Afternoon: 14:00-17:00 14:00-16:15 Practice: read mapping and variant calling (continued). Jordi Estellé and Purnima Pachori 16:15-16:45 Coffee break 16:45-17:15 Evaluation of the training school 17:30 Closing Claire Rogel-Gaillard and Nizar Drou
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Trainers and organizers Luca Fontanesi is Associate Professor of Animal Breeding and Genetics at the University of Bologna (Bologna, Italy) and Chair of COST Action "A Collaborative European Network on Rabbit Genome Biology - RGB-Net". Research interests: rabbit genomics, pig genomics (in general: livestock genomics). Contact e-mail: [email protected] Tahar Ait-Ali. The University of Edinburgh, Roslin Insitute (Scotland, UK). Chair of COST Action “ European Network for Understanding and Combating Porcine reproductive and respiratory syndrome in Europe” – EuroPERRS-Net Contact e-mail : [email protected] .ac.uk Claire Rogel-Gaillard works ate the National Institute of Agronomic Research (INRA) as a team leader in the Animal Genetics and Integrative Biology (GABI, ) unit in Jouy en Josas, France and as scientific adviser to the President of INRA. Species of interest: pig and rabbit. Fields of interest: immunogenetics, interactions between host and gut microbiota, structural and functional genomics, data integration. She is in charge of the work package entitled “Refinement of the European rabbit genome resource and development of genome-based platforms” for the RGB-Net COST Action. Contact e-mail: [email protected] Nizar Drou joined TGAC in 2009. He is the Sequence Assembly & Analysis Project leader. Nizar and his team work on de novo genome sequencing projects and reference aided resequencing projects on a range of organisms from viral and bacterial samples through to animal and plant genomes utilising the strengths and capabilities of 2nd (illumina, 454) and 3rd generation (PacBio) sequencing technologies. Applying high throughput bioinformatics techniques and the development of open source tools and resources is also an integral part of the Sequence Assembly & Analysis team's key objectives. Prior to joining TGAC, Nizar worked at the John Innes Centre Computational & Systems Biology group as a bioinformatics research scientist as part of the multinational Brassica rapa genome sequencing project.
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