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# Introduction to DNA Methylation data analysis
Joachim Wolff
Yvan Le Bras
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??? Presenter notes contain extra information which might be useful if you intend to use these slides for teaching. Press `P` again to switch presenter notes off Press `C` to create a new window where the same presentation will be displayed. This window is linked to the main window. Changing slides on one will cause the slide to change on the other. Useful when presenting. --- ## Requirements Before diving into this slide deck, we recommend you to have a look at: - [Introduction to Galaxy Analyses](/training-material/topics/introduction) - [Sequence analysis](/training-material/topics/sequence-analysis) - Quality Control: [
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hands-on](/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html) --- ## DNA Methylation data analysis ## -- ##Bisulfite sequencing QC and processing in Galaxy --- #Biological background ---  --- .image-75[] --- #Methylation: What is it good for? - Suppression of repeats - Gene expression - Imprinting - X-chromosome inactivation - Chromosome stability - Development - Changes in cancer - Changes with age --- #Heritable methylation .image-50[] .image-25[] <small>Weaver et al. Nature Neurosci 2004; 7: 847-854</small> --- #More than 5-mC .image-75[] <small>Mariani et al. (2013) Cancers</small> --- # [Hands-on](/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html) ##Step number 1: load data and run FastQC --- # Bisulfite sequencing .image-75[] --- # Mapping a bisulfite sequence read .image-75[] <small>Krueger et al.</small> --- # For the morbidly curious ####For SE datasets or read number 1 in PE: - C→T converted read: OT or OB (original strand) - G→A converted read: CTOT or CTOB (complementary strand) - C→T converted genome: OT or CTOB (top physical strand) - G→A converted genome: OB or CTOB (bottom physical strand) --- # [Hands-on](/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html) ##Step number 2: Alignment and methylation bias --- #Methylation bias .image-75[] --- #Methylation extraction ```txt track type="bedGraph" description="SRR1182519.sorted CpG Methylation levels" 1 25114 25115 100 2 1 1 25115 25116 100 3 1 track type="bedGraph" description="SRR1182519.sorted merged CpG Methylation levels" 1 25114 25116 100 5 1 ``` --- # [Hands-on](/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html) ##Step number 3: Visualization and more --- #Thanks for your attention! --- ## Related tutorials --- ## Thank You! This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!
Author(s)
Joachim Wolff
Yvan Le Bras
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