Introduction to DNA Methylation data analysis
Contributors
Authors:
Joachim Wolff
Yvan Le Bras
last_modification Last modification: Jul 26, 2021
DNA Methylation data analysis
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##Bisulfite sequencing QC and processing in Galaxy
#Biological background
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#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!