2016 05-29-intro-sib-springschool-leuker bad
TRANSCRIPT
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Spring-school in Bioinformatics & Population Genomics
(practical sessions)
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This changes everything.
Any lab can sequence anything!
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Genomics is taking over biology• Applied:
• Cancer genomics• Biodiversity assessments• Stool microbiome sequencing• Personalized medicine
• Research: • Development, • Evolution, • Ecology• … how life works!
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DATABIG
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Practicals Team
• 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__
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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.
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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.
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Virtual Machine?
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My favourite package?• Already:
• Claudia Kasper: RMarkdown
• Michel Moser: Jupyter Notebook
• Sina Rüeger: R stuff
• Kevin Daly: tmux
• Maybe you?
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