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2016 05-29-intro-sib-springschool-leuker bad

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Intro to practicals @ genomics course http://wurmlab.github.io/genomicscourse/2016-SIB/

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2016 05-29-intro-sib-springschool-leuker bad

  1. 1. Spring-school in Bioinformatics & Population Genomics (practical sessions)
  2. 2. This changes everything. Any lab can sequence anything!
  3. 3. Genomics is taking over biology • Applied: • Cancer genomics • Biodiversity assessments • Stool microbiome sequencing • Personalized medicine • Research: • Development, • Evolution, • Ecology • … how life works!
  4. 4. BIG
  5. 5. PracticalsTeam • Rob Waterhouse (Uni Geneva) - @rmwaterhouse • Julien Roux (Uni Lausanne) - @_julien_roux • Roddy Pracana (Queen Mary, London) @RoddyPracana • Stefan Schiffels (Max Planck, Jena) @stschiff • Yannick Wurm (Queen Mary, London) @yannick__
  6. 6. Practical sessions (Monday &Tuesday) • Reads to reference genome & gene predictions: • Short read cleaning, • genome assembly, • gene prediction, • quality control.
 • Population sequencing to genotypes to population genetics statistics: • Mapping reads, calling variants, visualizing variant calls. • Analysing variants: PCA, measuring diversity & differentiation.
  7. 7. Practical sessions (Weds &Thursday) • Inferring population sizes and gene flow
 • Gene expression: • From raw sequencing data to transcript expression levels. • Gene-level clustering and differential expression analysis.
  8. 8. Virtual Machine?
  9. 9. My favourite package? • Already: • Claudia Kasper: RMarkdown • Michel Moser: Jupyter Notebook • Sina Rüeger: R stuff • Kevin Daly: tmux • Maybe you?

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