Epigenomics Workshop 2022
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Pre-course Information
Online classroom
Schedule
Tutorials
Setup
DNA Methylation
ChIPseq
Downstream Processing
ATACseq
Advanced ChIP methods
Nextflow & nf-core
Data Integration
Experimental Design and Data Considerations
Epigenomics Workshop 2022
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Tutorials
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Tutorials
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Setup
Using computational resources
Directory structure
Commands and modules
Software Dependencies
DNA Methylation
Array workflow
Sequencing workflow
ChIPseq
ChIPseq: processing and narrow peak detection
ChIPseq: broad peaks detection
ChIPseq: alternative QC
Signal visualisation
Downstream Processing
Annotation using ChIPseeker
Detection of differential binding sites using DiffBind nd annotation with ChIPpeakAnno
Identification of sequence motifs
Detection of differential binding sites using csaw
ATACseq
ATACseq: processing and peak detection
Advanced ChIP methods
Setting up
CUT&RUN and ChIP data for CTCF
CUT&Tag H3K27me3 data
MINUTE-ChIP H3K27m3 data
Spike-in
Nextflow & nf-core
tmux
Setup: Nextflow
Setup: nf-core
Running a test workflow
Running a real workflow
CHiP-seq
Methyl-seq
Getting help
Data Integration
scATAC-seq analysis and integraion with scRNA-seq data
Genomic overlaps
BONUS EXERCISE: Unsupervised data integration
Experimental Design and Data Considerations
Public resources
Experiment design for ChIP-seq
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