Epigenomic Data Analysis (2016)

Course Objectives

A poster announcing this workshop can be found here

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.

Course Material

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Module 1 - Introduction to ChIP sequencing & analysis (2016) (Faculty: Martin Hirst)

application/pdf iconPDF (9MB) | application/vnd.openxmlformats-officedocument.presentationml.presentation iconPPT (10MB)

Module 2 - ChIP-seq alignment, peak calling & visualization (2016) (Faculty: Misha Bilenky)

application/pdf iconPDF (2MB)

Module 3 - Introduction to WGBS and analysis (2016) (Faculty: Guillaume Bourque)

application/pdf iconPDF (6MB) | application/vnd.openxmlformats-officedocument.presentationml.presentation iconPPT (7MB)

Module 4 - Downstream analyses & integrative tools (2016) (Faculty: David Bujold)

application/pdf iconPDF (7MB) | application/vnd.openxmlformats-officedocument.presentationml.presentation iconPPT (6MB)