Topic outline

  • General

    Chip-seq data analysis: from quality check to motif discovery and more - An introduction to the tools and databases of the EPD team

    Lausanne, 4-8 April 2016

    This page is addressed to registered participants. To access course description and application form, please click here.

    For any assistance, please contact

    • Program


      GA        Giovanna Ambrosini (EPD/EPFL/SIB)
      PB        Philipp Bucher (EPD/EPFL/SIB)
      RD       René Dreos (EPD/EPFL/SIB
      RG      Romain Groux (EPD/EPFL/SIB)
      SK        Sunil Kumar (EPD/EPFL/SIB)

      List of papers for students

      Doodle to validate your paper's choice

      • Monday morning

        Principles of ChIP-seq data analysis explained by a guided tour through the ChIP-seq and SSA server environment (GA)

        Practicals: Start going through the Basic ChIP-Seq and SSA Tutorial posted here.

        • Monday afternoon

          More about DNA motifs and position weight matrices. Introduction to the PWM tools (PB, GA)

          Practicals: Continue with the Basic ChIP-Seq and SSA Tutorial. If time permits, continue with ChIP-Seq Motif Tutorial which will be posted here.

          • Tuesday morning

            ChIP-Seq server – the nitty-gritty details: data representation, file formats, algorithms, parameter fine-tuning, interoperability with other servers (PB, GA)

            Practicals: ChIP-Seq Motif Tutorial part 1 to 4. Finish Basic Tutorial if you have not yet done so.  Both Tutorials are posted here.

            • Tuesday afternoon

              The Eukaryotic Promoter Database EPD: Design principles, source data, data files, web interfaces and integration with other tools. (RD)

              The practical for this session can be found here

              • Wednesday morning

                Working with public data: Organization and contents of the Mass Genome Annotation (MGA) data repository, introduction to genomic context analysis (RD, PB)

                Practicals: Go through parts 1and 2 of the ChIP-Seq, SSA and PWMTools Advanced tutorial. A  preliminary version of the tutorial can be found here.

                If you plan to work with your own data in the future, you may also do the uploading exercise posted here.

                • Wednesday afternoon

                  Data heterogeneity: Introduction to probabilistic partitioning and applications to ChIP-Seq data analysis data (SK, RG)

                  Practical exercises for the session can be found here.

                  • Thursday morning

                    Advanced applications: Motif dliscovery with SSA tools, PWM evaluation with ChIP-seq data, using ChIP-seq tools on Amazon cloud (PB, GA, SK)


                    • Go through part 5 othe ChIP-Seq Motifs tutoriall posted here.
                    • Go through part 3 of the Advanced tutorial posted  here .
                    • Thursday afternoon

                      Selected case studies in epigenomics using NGS-based and how to reproduce the corresponding results from these studies. Practical exercises for this session can be found here. (PB, GA, RD, RG, SK)

                      • Friday morning

                        Paper presentations by course participants.

                        • Friday afternoon

                          Paper presentations by course participants