Topic outline

  • General

    RNA-seq: from experiment planing to statistical data analysis

    Lausanne - 21-25 January 2013

    Next Generation Sequencing not only allows to sequence genomes, transcriptomes are also an important target. During this course, participants will discover all the necessary steps to run a successfull RNA-seq experiment and what biological knowledge can be generated from these experiments. They will learn to plan their experiment, choose the right technology, quality control and clean the raw data, assemble a transcriptome, identify isoforms, and analyse expression data with statistical tools. They will apply their knowledge practically under the supervision of lecturers and assistants. Requirements: Working knowledge of UNIX command-line and R/Bioconductor are essential to benefit from this course.


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    Organisers: Dr. Laurent Falquet, UNIFR Dr. Charlotte Soneson, SIB Lausanne Dr. Rémy Bruggmann, Philosophisch-naturwissenschaftliche Fakultät, UNIBE Dr. Michal Okoniewski, Functional Genomics Center Zurich, ETHZ

    • Topic 1

      Monday, January 21, 2013

      • Lecture and Exercises: Michal Okoniewski and Rémy Bruggmann

        9h00 Welcome to the participants

        9h15-12h00 Intro on gene expression, experiment planning, choice of technology (Microarray vs Seq, Illumina vs others).

        Visit of the sequencing facility in Bern, sample preparation



      • Lecture and Exercises Laurent Falquet and Michal Okoniewski

        13h30-17h30 UNIX & R refreshment.

    • Topic 2

      Tuesday, January 22, 2013

      • Lecture and exercises Laurent Falquet

        9h00-12h00 Quality Control of the data, error correction. De novo RNA Assembly (oases, Trans-abyss, SoapdenovoTrans, Trinity…)

      • Lecture and exercises Laurent Falquet

        13h30-17h30 Mapping (bowtie, bwa etc…) RPKM, FPKM, multireads matches or Unique ?

    • Topic 3

      Wednesday, January 23, 2013

      • Lecture and Exercises Rémy Bruggmann

        9h00-12h00 Reference based transcript reconstruction (Tophat, Cufflinks, MISO etc…)


      • Lecture and Exercises Charlotte Soneson

        13h30-17h30 Main statistial part, differential expression

    • Topic 4

      Thursday, January 24, 2013

      • Lectures and exercises Michal Okoniewski
        9h00-12h00 Splicing, transcript deconvolution,exon-intron junction detection, fusion or chimeric transcripts

      • Lectures and exercises Michal Okoniewski

        13h30-17h30 Functional analysis

    • Topic 5

      Friday, January 25, 2013

      • Lectures and exercises Charlotte Soneson

        9h00-12h00 Classification, other stats topics

      • Exam session
        13h30-16h30