ChIP-Seq

Keywords

ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation

Global learning objectives

• Describe the ChIP-Seq experimental and analysis workflow
• Apply suitable experimental design
• Apply suitable quality control
• Visualise raw and processed data
• Annotate, interpret and assess results

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Modules

Every module has had an Essential/Optional state assigned by the consortium.
Essential conveys the opinion that these modules should always be adressed in
any course/workshop about ChIP-Seq, i.e. they are the minimal set of modules
that a trainee has to learn about. The optional modules on the other hand may
be addressed depending on the workshop/course program/duration.

Preprocessing (Essential)

• Describe necessary preprocessing steps
• Apply QC software and interpret the result

Alignment (Essential)

• Use aligner software
• Discuss alignment considerations

ChIP-seq-QC (Essential)

• Explain ChIP-seq specific QC steps
• Perform ChIP-seq QC on a data set

Peak-calling (Essential)

• List appropriate peak-calling software
• Describe the theoretical basis of peak-calling
• Test different peak callers

Visualisation (Essential)

• Apply visualisation software to raw and processed data
• Assess data quality

Annotation (Optional)

• Interpret results in the genomic context

Differential-binding (Optional)

• Define an appropriate experimental and analysis design
• Discuss normalization strategies
• Perform differential binding analysis
• Interpret results

Working with biological replicates (Optional)

• Compare and combine different biological replicates using IDR analysis

Non-peak based analysis (Optional)

• Inspect signal around regions of interest
• Generate carpet plots

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