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, 27 April - 1 May 2015


    This is a course on bioinformatics resources taught by the developers of the resources. Participants will learn how to analyze their own or public ChIP-seq data using tools from the ChIP-seq, Signal Search Analysis (SSA) and PWMtools servers in conjunction with the Eukaryotic Promoter Database (EPD) and external regulatory bioinformatics tools. 


    After the course, participants should have a thorough understanding of the methods of ChIP-seq data analysis and DNA motif-based gene regulatory region analysis. They should be proficient in the usage of our bioinformatics tools and be able to interpret results obtained with our tools. Moreover, they should have gained ample practical experience in working with public NGS-based functional genomics data.       


    Skills: participants should have a good understanding of molecular biology and functional genomics. Most of the exercises are web-based. Basic knowledge of R is required for some exercises, please visit our tutorial here.

    Material requirements: A WiFi-equipped laptop with 30 GB free hard-disk space.  


    The registration fees for academics are 200 CHF. This includes course content material and coffee breaks. Participants from non-academic institutions should contact us before application.

    Application is now closed.

    Deadline for registration and free-of-charge cancellation is set to April 22. Cancellation after this date will not be reimbursed.


    The course will take place at EPFL in room AAC006 from 9:00 to 17:30 during the period April 27 - May 1, 2015, except April 30 when the course will be held in room AAC008.

    Additional information

    The course is worth 2 ECTS credits (40 hours lessons/practical + 20 hours paper preparation / presentation).

    The list of papers for the Friday sessions is posted here. Please select your paper via the doodle poll. Presenting a paper is mandatory for students who take the course for credits and highly encouraged for all other participants.

    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.

    Students presentations

    The timetable for Friday students' presentations can be found here

    • Preliminary program


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


    • Monday morning

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


      • Monday afternoon

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


        • Tuesday morning

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


          • Tuesday afternoon

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


            • Wednesday morning

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


              • Wednesday afternoon

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


                • Thursday morning

                  More on the ChIP-seq and SSA server tools: Advanced applications and interoperability with other bioinformatics resources tools. (PB, GA)


                  • Thursday afternoon

                    Selected case studies in epigenomics using NGS-based and how to reproduce the corresponding results from these studies (PB, GA, DR, SK)


                    • Friday morning

                      Paper presentations by course participants.


                      • Friday afternoon

                        Paper presentations by course participants