ChIP-Seq

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

Top | Keywords | Objectives | Modules

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

ChIP-Seq https://tess.elixir-europe.org/materials/chip-seq No description available ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation