Integrated ChIP-seq Data Analysis Workshop

Instructors name and contact information

• Kai Hu: kai.hu@umassmed.edu
• Jianhong Ou: jianhong.ou@duke.edu
• Rui Li: rui.li@umassmed.edu
• Haibo Liu: haibol2017@gmail.com
• Lihua Julie Zhu: julie.zhu@umassmed.edu

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.

Pre-requisites

• 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

• Install Docker (https://www.docker.com/)
• Pull the Docker image from Docker hub: docker pull hukai916/integratedchipseqanalysis_workshop
• Run the image: docker run -e PASSWORD=yourpassword -p 8787:8787 hukai916/integratedchipseqanalysis_workshop
• Log in to RStudio at http://localhost:8787 using username rstudio and password yourpassword. For Windows users, you also need to provide your IP address, you can find it using docker-machine ip default.
• Inside the RStudio, run: browseVignettes(package = "hukai916/integratedchipseqanalysis_workshop")
• You can click one of the links: "HTML", "source", "R code"
• In case of The requested page was not found error, try add 'help/' in front of the hostname in the URL (this is a known bug): http://localhost:8787/help/library/integratedchipseqanalysisworkshop/doc/IntegratedChIPseqAnalysisWorkshop.html

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

Useful links

• pkgdown website that contains all workshop materials: https://hukai916.github.io/IntegratedChIPseqWorkshop
• docker image that contains all dependencies required for the workshop: https://hub.docker.com/repository/docker/hukai916/integratedchipseqanalysis_workshop
• GitHub Action build status badge:

References

[1] https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

[2] https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html

[3] https://bioconductor.org/packages/release/bioc/html/trackViewer.html

[4] http://bioconductor.org/packages/release/bioc/html/MotifDb.html

[5] https://bioconductor.org/packages/release/bioc/html/ChIPQC.html

[6] https://bioconductor.org/packages/release/bioc/html/DiffBind.html

[7] https://bioconductor.org/packages/release/bioc/html/csaw.html

[8] https://www.bioconductor.org/packages/release/bioc/html/rGADEM.html

[9] https://bioconductor.org/packages/release/bioc/html/motifStack.html

[10]https://bioconductor.org/packages/release/bioc/html/GeneNetworkBuilder.html