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.
  • Attendees are strongly encouraged to bring a laptop computer capable of accessing UCLA’s WiFi.


Daria Merkurjev is a postdoc at UCLA working in the laboratories of Dr. Jake Lusis, Dr. Caius Radu, and Dr. Grace Xiao. Dr. Daria Merkurjev did her undergraduate work in Mathematics at UCLA and has received her Ph.D. in Bioinformatics and Systems Biology at UCSD under Dr. Michael Rosenfeld. Her Ph.D. research focused on investigating the molecular and architectural strategies responsible for integrating genome-wide transcriptional responses to diverse signaling systems critical for physiological and behavioral processes in vertebrates. Her research also includes understanding the factors affecting susceptibility to cardiovascular and metabolic disorders.



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!


Workshop Details

Prerequisites: W1, 2, & 4
Length: 3 days, 3 hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 15

Fall 2018 Dates

Sorry! Will return in Winter 2019.