Genome Annotation - Genome Annotation
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
Genome Annotation - Genome Annotation
http://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/genome-annotation/tutorial.html
http://tess.elixir-uk.org/materials/genome-annotation-genome-annotation
Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.
joachimwolff
erxleben
bgruening
Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
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.
Questions of the tutorial:
- Why is a Hi-C analysis useful?
- What is...
Epigenetics - Hi-C analysis of Drosophila melanogaster cells using HiCExplorer
http://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/hicexplorer/tutorial.html
http://tess.elixir-uk.org/materials/epigenetics-hi-c-analysis-of-drosophila-melanogaster-cells-using-hicexplorer
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.
Questions of the tutorial:
- Why is a Hi-C analysis useful?
- What is 'chromosome conformation capture'?
- What are main steps in order to generate and plot a Hi-C contact matrix?
joachimwolff
fidelram
vivekbhr
polkhe
Introduction to Galaxy Analyses - IGV Introduction
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Introduction to Galaxy Analyses - IGV Introduction
http://galaxyproject.github.io/training-material/topics/introduction/tutorials/igv-introduction/tutorial.html
http://tess.elixir-uk.org/materials/galaxy-introduction-igv-introduction
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
nekrut
joachimwolff
pajanne
ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
ChIP-sequencing is a method used to analyze protein interactions with DNA.
Questions of the tutorial:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of Tal1?
- Which genes are regulated by Tal1?
Objectives of the tutorial:
- Inspect read quality with FastQC
-...
ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
http://galaxyproject.github.io/training-material/topics/chip-seq/tutorials/tal1-binding-site-identification/tutorial.html
http://tess.elixir-uk.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-t-cell-acute-lymphocytic-leukemia-protein-1-tal1
ChIP-sequencing is a method used to analyze protein interactions with DNA.
Questions of the tutorial:
- How is raw ChIP-seq data processed and analyzed?
- What are the binding sites of Tal1?
- Which genes are regulated by Tal1?
Objectives of the tutorial:
- Inspect read quality with FastQC
- Perform read trimming with Trimmomatic
- Align trimmed reads with BWA
- Assess quality and reproducibility of experiments
- Identify Tal1 binding sites with MACS2
- Determine unique/common Tal1 binding sites from G1E and Megakaryocytes
- Identify unique/common Tal1 peaks occupying gene promoters
- Visually inspect Tal1 peaks with Trackster
malloryfreeberg
moheydarian
vivekbhr
joachimwolff
erxleben
Epigenetics - DNA Methylation data analysis
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.
Questions of the tutorial:
- What is methylation and why it cannot be...
Epigenetics - DNA Methylation data analysis
http://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html
http://tess.elixir-uk.org/materials/epigenetics-dna-methylation-data-analysis
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.
Questions of the tutorial:
- What is methylation and why it cannot be recognised by a normal NGS procedure?
- Can a different methylation influence the expression of a gene? How?
- Which tools you can use to analyse methylation data?
Objectives of the tutorial:
- Learn how to analyse methylation data
- Get a first intuition what are common pitfalls.
joachimwolff
dpryan79
Epigenetics - Introduction to DNA Methylation data analysis
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.
Epigenetics - Introduction to DNA Methylation data analysis
http://galaxyproject.github.io/training-material/topics/epigenetics/slides/introduction.html
http://tess.elixir-uk.org/materials/epigenetics-introduction
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.
joachimwolff
yvanlebras
Sequence analysis - Mapping
Analyses of sequences
Questions of the tutorial:
- What two things are crucial for a correct mapping?
- What is BAM?
Objectives of the tutorial:
- You will learn what mapping is
- A genome browser is shown that helps you to understand your data
Sequence analysis - Mapping
http://galaxyproject.github.io/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html
http://tess.elixir-uk.org/materials/analysis-of-sequences-mapping
Analyses of sequences
Questions of the tutorial:
- What two things are crucial for a correct mapping?
- What is BAM?
Objectives of the tutorial:
- You will learn what mapping is
- A genome browser is shown that helps you to understand your data
joachimwolff
