ChIP-Seq course

Differential protein binding to DNA using ChIP-Seq data and the Galaxy platform

Your profit: This course covers topics regarding experimental design of ChIP-Seq experiments, introduction and considerations for NGS sequencing, hands on sessions to get from raw sequencing data to peaks using the Galaxy platform [1], QCs, sample visualizations and the statistical analyses of differential protein binding to DNA using R and the DiffBind package [2]. You will create an integrated report using RStudio and R Markdown [3] and have the opportunity to analyze your own data or a published dataset of interest.

Topics

  • Introduction to RMarkdown (Day1)
  • Fundamentals of ChIP-seq analysis
  • Processing of ChIP-seq data using Galaxy
  • Visualization of sequencing data and analysis of ChIP-Seq data with DiffBind
  • Integrated ChIP-Seq data analysis with R and RStudio

    Methods: Presentations, Hands-on sessions and exercises, Homework assignment, Q&A sessions
    Mode: During the Corona-pandemic the course is held as an online course
    Requirements:
    Introduction to R or equivalent course/experience
    Duration:
    3 Days
    Language:
    English

    Dates and Application
    You can check the current dates and whether the courses are already fully booked here*.
    Please apply via the forms of the HR Development department*.

    References
    [1] galaxyproject.org
    [2] Ross-Innes CS et al. (2012). Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature, 481(7381): 389–393. dx.doi.org/10.1038/nature10730
    [3] rstudio.com, https://rmarkdown.rstudio.com

    * Links marked with * are only available for HMGU staff.