Introduction to DNA Methylation data analysis

Contributors

Authors: Joachim Wolff Yvan Le Bras

DNA Methylation data analysis

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##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

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Weaver et al. Nature Neurosci 2004; 7: 847-854

#More than 5-mC .image-75[]

Mariani et al. (2013) Cancers

Hands-on

##Step number 1: load data and run FastQC

Bisulfite sequencing

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Mapping a bisulfite sequence read

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Krueger et al.

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

##Step number 2: Alignment and methylation bias

#Methylation bias .image-75[]

#Methylation extraction

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

##Step number 3: Visualization and more

#Thanks for your attention!

Thank you!