Workshop Description

Higher-order chromatin structure is being increasingly recognized as a critical component of gene regulation. Long-range chromatin interactions can be detected using Hi-C, a genome-wide derivative of the chromosome conformation capture (3C) assay. This three-day workshop is designed to provide an introduction to Hi-C analysis.

Day 1

  • Introduction to the 3D genome
  • Overview of Hi-C experiments: wet lab and computational consideration
  • Quick review of linux, Hoffman2 and high-throughput sequencing glossary.
  • Aligning Hi-C library using HiC-Pro

Slides for day 1 can be found here.

Day 2

  • Aligning Hi-C library using HiC-Pro, continued.
  • Visualization of data using HiC-Plotter

Slides for day 2 can be found here.

Day 3

  • Identification of significant chromatin interactions using GOTHiC.
  • Calculate directionality index using HiTC.
  • Overview of other useful Hi-C tools: hicup, HOMER

Slides for day 3 can be found here.

Technical Requirements

Computer with access to UCLA WIFI with the following installed and tested:

  • an SSH client to access the Hoffman2 cluster (for Windows, use PuTTY). Users must have Hoffman2 active user account.
  • a SFTP file transfer software such as FileZillaCyberduckor WinSCP

You should be already familiar with these softwares from previous workshops. In the interest of timeliness, we cannot troubleshoot each and everyone’s configuration, so please make sure that everything is working before coming to class, or you won’t be able to practice. All the other tools required for Hi-C specific analysis will be accessed through Hoffman2.


Fides Lay is a postdoctoral fellow in the laboratory of Dr.Hanna Mikkola. Her current research focuses on elucidating the transcriptional machineries controlling fate commitment and self-renewal during normal hematopoiesis and understanding how these processes are hijacked during leukemogenesis. When not in lab, she enjoys running, kickboxing, going to concerts, eating unhealthy amount of chocolates, and basking in the warm Los Angeles sun.

 Email: or

Education: B.Sc. Biochemistry UCLA 2008; Ph.D. Genetics, Molecular and Cell Biology USC 2014

Workshop Details

Prerequisites: W1, 2, & 3 or
basic Unix and R scripting
W9 is strongly recommended
Length: 3 days, 2 hrs per day
Level: Advanced
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 10

Fall Dates

Nov. 28 – 30, 1 – 4pm