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.

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