This course builds on the core skills introduced in the Introduction to R, Introduction to Unix and Introduction to SeqMonk courses to provide a more in depth look at the analysis of bisulphite sequencing data. The course is a mix of theoretical lectures and hands on practicals which go through the whole analysis pipeline, starting from raw sequence data and covering QC, visualisation, quantitation and differential methylation analysis.

Course Content

• The theoretical basis for BS-Seq
• Processing raw sequencing data with Bismark
• Visualisation and exploration of methylation calls with SeqMonk
• The theory of differential methylation calling
• Differential methylation analysis practical

Course Material

• BS-Seq data processing lecture (pptx)
• BS-Seq data processing lecture (pdf)
• BS-Seq data processing exercises (docx)
• BS-Seq data processing exercises (pdf)
• Visualisation and exploration lecture (pptx)
• Visualisation and exploration lecture (pdf)
• SeqMonk tools for methylation analysis (pptx)
• SeqMonk tools for methylation analysis (pdf)
• Visualisation and exploration practical (docx)
• Visualisation and exploration practical (pdf)
• Differential methylation lecture (pptx)
• Differential methylation lecture (pdf)
• Differential methylation practical (docx)
• Differential methylation practical (pdf)
• ox-BS-Seq lecture (pptx)
• ox-BS-Seq practical (pdf)
• Data for all practicals (tar.gz, WARNING 14GB)