Topic outline

  • General

    Statistical genetics and statistical genomics

    Lausanne, 3-6 February 2014

    Overview

    This course provides an introduction to various topics in statistical genetics and statistical genomics, with a special focus on widely used software and tools developed by researchers at SIB.

    The topics covered by the course include: population genetics, genome-wide association studies, differential expression analysis of gene expression data obtained by microarrays or RNAseq, analysis of ChIP-seq and 4C-seq data and integration of multiple genome-wide data sets.

    Objectives

    The course will consist of lectures and computer exercises, where the participants apply the acquired knowledge. At the end of the course the participants should have a deeper understanding of the basic concepts and methodologies used in statistical genetics and statistical genomics, and be able to perform analyses using the tools presented during the course.

    Requirements 

    Basic knowledge of genetics, unix (UNIX Fundamentals self-learning module) and R is required to attend the course.
    Bring laptop with wifi enabled, at least 4GB of RAM and virtualbox installed. You will be given a virtual machine image with all software and packages needed for this course.

    Registration 

    Registration is now closed (the course is full).
    The registration fees for academics are 200 CHF. The fees include course content material, coffee breaks and a social dinner. Participants from non-academic institutions should contact us. Deadline for registration and cancellation is set to the 20th of January 2014.

    Additional information

    You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

    We will recommend 2 ECTS credits for this course.

    Location

    For more information, please contact training@isb-sib.ch

    • Monday 3 February 2014

      Morning session

      Population genetics (Matthieu Foll (slides), Greg Ewing (slides))

      Exercises

      Software needed for exercises (already installed in virtual machine):

      msms: http://www.mabs.at/ewing/msms/download.shtml

      Afternoon session

      Genetic diversity (Niko Beerenwinkel (slides))

      Exercises

      Data

      Software needed for exercises (already installed in virtual machine):

      bwa 0.7.5a: http://bio-bwa.sourceforge.net/

      samtools: http://sourceforge.net/projects/samtools/files/

      InDelFixer 1.1: https://github.com/armintoepfer/InDelFixer/releases

      Tablet: http://bioinf.scri.ac.uk/tablet/download.shtml

      QuasiRecomb: https://github.com/armintoepfer/QuasiRecomb/releases

      QuasiFit: https://github.com/SoapZA/QuasiFit/releases

      Exam

      • Tuesday 4 February 2014

        Morning session

        Gene expression analysis (microarrays and RNA-seq) (Mark Robinson (slides))

        Exercises

        Afternoon session

        ChIP-seq and 4C-seq data analysis (Jacques Rougemont (slides))

        Exercises

        Data for the "3.Try it yourself" section:

        Please download within the Virtual Machine either the .tar.gz file (1.2 Gb plus 3Gb once uncompressed) here or each file separately from here

        Exam

        Social dinner at les Brasseurs @ 7 p.m

        • Wednesday 5 February 2014

          Morning session

          Genome-wide association studies (Zoltán Kutalik (slides1,slides2))

          Exercises

          Afternoon session

          eQTL analysis, exploratory analysis of gene expression data, alternative splicing analysis (Alfonso Alberto Buil Demur (slides), Pedro Dias Ferreira (slides))

          Exam

          • Thursday 6 February 2014

            Morning session

            "System analysis": data integration and network analysis (Sven Bergmann)

            Afternoon session

            Integration of multiple omics data types (Pratyaksha Wirapati (slides))

            Exercise

            Exam