Workshop Description (Intermediate Course)

This workshop aims to provide skills needed to address principles of the assay, quality assessment, sequencing depth, data processing and functional downstream analyses of ChIP-seq datasets. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.

Workshop Topics

•Assay protocol
•Principles and theory
•Quality Control
•Data download from GEO (SRA toolkit)

•Alignment to human genome (Bowtie2)
•Peak calling (MACS)
•Genome browser viewing (IGB)
•Differential peak calling (HOMER)

•ChIP region annotation (CEAS)
•Peak overlap between datasets (SITEPRO/BEDtools)
•Integrative RNA-seq promoter analysis (CEAS)
•TF Motif discovery (HOMER)
•Gene assignment and gene ontology (GREAT)

For the workshop slides, please click below.

Day 1- ChIP Seq - Day 1

Day 2 and 3- ChiP Seq Day 2 and 3

Technical Requirements

  • Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.
  • We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.


Dr. Weihong Yan is the system administrator of Galaxy. She constructs and maintains software and hardware needed for bioinformatics application. Dr. Wang provides consultation services on microarray, proteomic and genomic data analysis. Email:



This was a great workshop that shows the various steps and options for representing and analyzing ChIP-seq data. The outline of the overall workshop made sense and provided me with a lot of information to try. Thanks!

He is a great instructor and very helpful with questions throughout the course.

I was glad that we went over QC methods and tools.

This is a good workshop for biologists to understand the analysis process of ChIP-seq data.

Workshop Details

Prerequisites: Intro to Unix (W1), & Using NGS Analysis Tools (W2)
Length: 3 days, 3 hrs per day
Level: Intermediate
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 15

Spring 2024 Dates

May 7, 8, and 9
1:30 PM – 4:30 PM