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.


To be announced


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

Winter 2019 Dates

Sorry! Will return in Spring 2019.