Epigenomic Data Analysis

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Course Objectives

High-throughput sequencing of Chromatin-Immunoprecipitated libraries (ChIP-seq) and of bisulfite converted DNA (WGBS) have become increasingly common and have largely supplanted microarrays for chromatin and DNA methylation profiling. When processed appropriately, ChIP-seq data provides base-pair resolution representations of transcription factor DNA-binding events and nucleosome (histone) modifications genome-wide. Similarly, WGBS can provide a quantitative genome wide profile of cytosine methylation.

The CBW has developed a 2-day course providing an introduction to histone ChIP-seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChIP-Seq and WGBS analysis packages. The tutorials are designed as self-contained units that include example data and detailed instructions for installation of all required bioinformatics tools (FASTQC, BWA, MACS2, FindER, samtools, Picard, BisSNP). The course also includes an overview of integrative epigenomic tools that have been developed to explore ChIP-Seq and WGBS data together with other epigenomic datasets such as RNA-seq, DHS-seq and ATAC-seq.

Participants will gain practical experience and skills to be able to:

  • Align ChIP-seq and WGBS sequence data to a reference genome (required)
  • Identify narrow and broad peaks from ChIP-seq data
  • Identify methylated levels from WGBS data
  • Visualize and summarize the output of ChIP-Seq and WGBS analyses
  • Explore integrative tools for epigenomic data sets

Target Audience

Graduates, postgraduates and PIs working with or about to embark on an analysis of epigenomic data and in particular of ChIP-Seq and Whole-Genome Bisulfite Sequencing (WGBS) experiments. Attendees may be familiar with some aspect of ChIP-Seq or WGBS data analysis or have no direct experience. A reference genome is required and we will be working on human data sets.

Prerequisites: Basic familiarity with Linux environment and S, R, or Matlab. Must be able to complete and understand the following simple Linux and R tutorials (up to and including “Descriptive Statistics”) before attending:

You will also require your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 2GB RAM, 10GB free disk space, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements).If you do not have access to your own computer, you may loan one from the CBW. Please contact course_info@bioinformatics.ca for more information.

Pre-work and pre-readings can be found at https://bioinformaticsdotca.github.io/epigenomics_2018.

Course Material