DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.
Before diving into this topic, we recommend you to have a look at:
- Introduction to Galaxy Analyses
- Sequence analysis
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Introduction to ChIP-Seq data analysis
Introduction to DNA Methylation data analysis
ATAC-Seq data analysis
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DNA Methylation data analysis
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EWAS data analysis of 450k data
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Formation of the Super-Structures on the Inactive X
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Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
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You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
You can also use the following Docker image for these tutorials:
docker run -p 8080:80 quay.io/galaxy/epigenetics-training
NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.
It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password admin to access everything.
This material is maintained by:Joachim Wolff, Devon Ryan
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
This material was contributed to by:Bérénice Batut, Joachim Wolff, Yvan Le Bras, Lucille Delisle, Maria Doyle, Florian Heyl, Devon Ryan, Katarzyna Murat, Krzysztof Poterlowicz, Friederike Dündar, Anika Erxleben, Vivek Bhardwaj, Fidel Ramirez, Leily Rabbani, Ekaterina Polkh