Workshop Description

A three-day workshop for hands-on analysis of genome-wide DNA methylation profiles.

In this workshop, we will learn about various tools available for WGBS data analysis, including alignment, methylation calling, identification of differentially methylated regions (DMRs), and visualization. The workshop will include hands-on learning and in-depth discussion of experimental design, data interpretation, advantages and disadvantages of multiple tools.

Day 1

  • Introduction to DNA methylation & WGBS experimental consideration
  • Quick review of linux, Hoffman2 and high-throughput sequencing glossary.
  • Aligning WGBS reads using bwa-meth

Slides

Day 2

  • DNA methylation calling using Bis-SNP
  • Analysis of differentially methylated regions (DMRs) using metilene
  • Visualization of data: IGV, plotting

Slides

Day 3

  • WGBS data analysis using BS-Seeker2: alignment and methylation calling

Slides

Technical Requirements

  • Attendees are required to have a Hoffman2 account. To apply for an account, click here.
  • We will be using the computers in the classroom, which have all the necessary software installed. To access the Hoffman2 cluster from your computer, you will need a Unix terminal. Mac has unix built in. For windows users, you need to use a unix terminal emulator such as Winscp, PUTTY and PSCP http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html 

Instructor

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: fidlay@ucla.edu or lay.fides@gmail.com

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

Workshop Details

Prerequisites: W1, 2 & 3, or
basic Unix or programming experience
Length: 3 days, 3 hrs per day
Level: Advance
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Fall Dates

Oct. 17 – 19, 1 – 4pm