View markdown source on GitHub

Introduction to DNA Methylation data analysis


last_modification Last modification: Jul 26, 2021

DNA Methylation data analysis

##Bisulfite sequencing QC and processing in Galaxy

#Biological background

Cartoon of a mitotic chromosome zoomed in to show dna and histones and nucleosomes, further zoomed in to show individual DNA strands with methylated dna.

.image-75[A picture from a paper with at top a cartoon of a chromosome and the chromatin, pointing to a single nucleosome, and the histone and dna methylation modifications possible. Below is a comparison of a switched on gene with active or open chromatin and unmethylated cytosines, and acetylated histones. Below is a switched off gene with condensed chromatin, methylated cytosines, and deacetylated histones.]

#Methylation: What is it good for?

#Heritable methylation

.image-50[Another paper chart, here a number of graphs are shown, but their interpretation is unclear.] .image-25[Another set of graphs from the same paper and a picture of a mouse and its baby suggesting heritability.]

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

#More than 5-mC .image-75[A schematic of a chemical pathway affecting cytosine and various transformation that can occur. Some have arrows indicating gene silencing or activation.]

Mariani et al. (2013) Cancers


##Step number 1: load data and run FastQC

Bisulfite sequencing

.image-75[Cartoon of a methlated gene sequence and bisulfite conversion  replacing a C with a U. Below that is sequenced and the resut is reconstructed to figure out which Cs were methylated (because they weren't replaced with Us.). ]

Mapping a bisulfite sequence read

.image-75[Illegible graphic from a paper showing reconstruction of methylated sequences.]

Krueger et al.

For the morbidly curious

####For SE datasets or read number 1 in PE:


##Step number 2: Alignment and methylation bias

#Methylation bias .image-75[line chart showing position along mapped read and CpG methylation percent. It is a wavy overlapping set of lines.]

#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


##Step number 3: Visualization and more

#Thanks for your attention!

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! Galaxy Training Network This material is licensed under the Creative Commons Attribution 4.0 International License.