name: inverse layout: true class: center, middle, inverse <div class="my-header"><span> <a href="/training-material/topics/epigenetics" title="Return to topic page" ><i class="fa fa-level-up" aria-hidden="true"></i></a> <a class="nav-link" href="https://github.com/galaxyproject/training-material/edit/master/topics/epigenetics/slides/introduction-dna-methylation.html"><i class="fa fa-pencil" aria-hidden="true"></i></a> </span></div> <div class="my-footer"><span> <img src="/training-material/assets/images/GTN-60px.png" alt="Galaxy Training Network" style="height: 40px;"/> </span></div> --- # Introduction to DNA Methylation data analysis --- ## 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) .footnote[Tip: press `P` to view the presenter notes] ??? 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. --- ## 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   --- # [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://wiki.galaxyproject.org/Teach/GTN) and all the contributors! <div class="contributors-line"> <a href="/training-material/hall-of-fame/joachimwolff/" class="contributor-badge"><img src="https://avatars.githubusercontent.com/joachimwolff" alt="Joachim Wolff">Joachim Wolff</a>, <a href="/training-material/hall-of-fame/yvanlebras/" class="contributor-badge"><img src="https://avatars.githubusercontent.com/yvanlebras" alt="Yvan Le Bras">Yvan Le Bras</a> </div> <img src="/training-material/assets/images/GTN.png" alt="Galaxy Training Network" style="height: 100px;"/> This material is licensed under the <a rel="license" href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.