Introduction to DNA Methylation data analysis

name: inverse
layout: true
class: center, middle, inverse

</span></div>

</span></div>

---

# Introduction to DNA Methylation data analysis

<div class="contributors-line">
		Authors: <a href="/training-material/hall-of-fame/joachimwolff/" class="contributor-badge contributor-joachimwolff"><img src="https://avatars.githubusercontent.com/joachimwolff?s=27" alt="Avatar">Joachim Wolff</a><a href="/training-material/hall-of-fame/yvanlebras/" class="contributor-badge contributor-yvanlebras"><img src="/training-material/assets/images/orcid.png" alt="orcid logo"/><img src="https://avatars.githubusercontent.com/yvanlebras?s=27" alt="Avatar">Yvan Le Bras</a>
	</div>

</div>

<div class="footnote" style="bottom: 8em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: </div>

<div class="footnote" style="bottom: 6em;">

<i class="fas fa-file-alt" aria-hidden="true"></i><span class="visually-hidden">text-document</span><a href="slides-plain.html"> Plain-text slides</a>
</div>

<div class="footnote" style="bottom: 2em;">
    <strong>Tip: </strong>press <kbd>P</kbd> to view the presenter notes
    | <i class="fa fa-arrows" aria-hidden="true"></i><span class="visually-hidden">arrow-keys</span> Use arrow keys to move between slides

</div>

???
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: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html)
    - Mapping: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/mapping/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html)

---

## 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.](../images/genome_organization.jpeg)

---

.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.](../images/modification_methylation.jpeg)]

---

#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[![Another paper chart, here a number of graphs are shown, but their interpretation is unclear.](../images/heritable_methylation.png)]
.image-25[![Another set of graphs from the same paper and a picture of a mouse and its baby suggesting heritability.](../images/mouse.jpg)]

<small>Weaver et al. Nature Neurosci 2004; 7: 847-854</small>

---

#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.](../images/more_than_5-mC.png)]

<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[![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.)](../images/bisulfite_sequencing.png)]

---

# Mapping a bisulfite sequence read
.image-75[![Illegible graphic from a paper showing reconstruction of methylated sequences.](../images/Mapping_a_bisulfite_seq_read.jpeg)]

<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[![line chart showing position along mapped read and CpG methylation percent. It is a wavy overlapping set of lines.](../images/methylation_bias.png)]

---

#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!

</div>

</div>

<a rel="license" href="https://creativecommons.org/licenses/by/4.0/">
This material is licensed under the Creative Commons Attribution 4.0 International License</a>.