Epigenetics
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.
Requirements
Before diving into this topic, we recommend you to have a look at:
- Introduction to Galaxy Analyses
-
Sequence analysis
- Quality Control: slides slides - tutorial hands-on
- Mapping: slides slides - tutorial hands-on
Material
Lesson | Slides | Hands-on | Input dataset | Workflows | Galaxy tour | Galaxy instances |
---|---|---|---|---|---|---|
Introduction to ChIP-Seq data analysis
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slides Toggle Dropdown | |||||
Introduction to DNA Methylation data analysis
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slides Toggle Dropdown | |||||
ATAC-Seq data analysis
|
tutorial Toggle Dropdown | zenodo_link | workflow | instances | ||
DNA Methylation data analysis
|
tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour | instances | |
Formation of the Super-Structures on the Inactive X
|
slides Toggle Dropdown | tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour | instances |
Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
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tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour | ||
Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
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tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour | instances | |
Infinium Human Methylation BeadChip
|
slides Toggle Dropdown | tutorial Toggle Dropdown | zenodo_link | interactive_tour |
Galaxy instances
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 password to access everything.
Maintainers
This material is maintained by:
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
Contributors
This material was contributed to by: