Workshop Description

This workshop aims to provide skills needed to address experimental reproducibility, sequencing depth, data reporting and quality assessment of ChIP-seq data. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.

Day 1

  • Cross-correlation analysis and ENCODE QC with SPP
  • BigWig tracks with defined resolution and normalization using
  • Homer/UCSC tools, and visualization with IGV
  • Peak calling with MACS2

Slides for all 3-days can be found here.

Day 2

  • QC of replicates with ENCODE’s IDR
  • Differential peak calling with MAnorm
  • Location annotation with NGSPLOT

Slides for all 3-days can be found here.

Day 3

  • Functional annotation with GREAT
  • Motif analysis with HOMER
  • Command-line tools to work more efficiently
  • Open Q&A

Slides for all 3-days can be found here.

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. Nathan Zemke is currently a post-doc in the Lab of Professor Arnie Berk in the Microbiology, Immunology, & Molecular Genetics department at UCLA. He received his bachelor’s degree in molecular biology at UCSD. He earned his PhD from the Molecular Biology Interdepartmental program at UCLA researching the adenovirus oncoprotein e1a and its regulation of chromatin, innate immune responses, and differentiation. 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!

Fall 2017 Student
 Daria was a great instructor and very helpful with questions throughout the course.
Spring 2017 Student

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

Spring 2017 Student

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

Spring 2017 Student

Workshop Details

Prerequisites: W1, W2, W& 4
Length: 3 days, 3 hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 15

Fall 2019 Dates

November 12, 13, and 14, 2019
1:30 PM to 4:30 PM