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="fa 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="fa 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="fa fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/mapping/slides.html) - [<i class="fa 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 --- ## 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;"/>