Instructors name and contact information

Workshop description

ChIP-seq combines chromatin immuno-precipitation (ChIP) with next-generation sequencing technology to analyze protein interactions with DNA. It has been widely adopted by biologists to identify transcription factor binding location and to map specific histone modification or nucleosome position on the genome. A typical workflow of ChIP-seq includes experimental design, sequencing, and downstream bioinformatics analysis. This workshop focuses on the bioinformatics part by comparing popularly practiced tools, their advantages and limitations. Specifically, we will demonstrate how to perform downstream analysis (after peak calling) with package ChIPpeakAnno and trackViewer.


  • General understanding of ChIP-seq analysis or have strong interests
  • Basic knowledge of R or Python
  • Familiar or have interests in the following concepts:
    • Short read mapping
    • Peak calling/annotation
    • Motif analysis
  • A computer that runs on Unix-like system

Workshop participation

A mini-lecture will be given at the beginning that will cover basic ideas behind ChIP-seq, comparision of commonly used tools for ChIP-seq data analysis. Then, a hands-on demo will be performed to demonstrate the downstream analysis with ChIPpeakAnno and trackViewer packages. Last will be a Q/A section.

How to run Docker

R / Bioconductor packages used

  • ChIPpeakAnno [1]
  • ATACseqQC [2]
  • trackViewer [3]
  • MotifDb [4]
  • ChIPQC [5]
  • diffbind [6]
  • csaw [7]
  • rGADEM [8]
  • motifStack [9]
  • GeneNetworkBulider [10]

Time outline

Activity Time
Overview of ChIP-seq 3m
Pipeline for ChIP-seq analysis 2m
Comparison of popular tools 5m
* short read aligner
* peak caller
Downstream analysis 10m
* peak annotation
* motif analysis
* metagene visualization
* etc.
Hands-on demonstration 25m
Q/A section 5m

Workshop goals and objectives

Learning goals

  • Describe the basic idea behind ChIP-seq
  • Identify the commonly practiced tools used in ChIP-seq analysis
  • Undertand the main challenges regarding ChIP-seq analysis

Learning objectives

  • Get familiar with the package ChIPpeakAnno and trackViewer
  • Explore peak annotation
  • Perform GO enrichment analysis
  • Perform metagene visualization
  • Identify binding motif