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

  • 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 
  • 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.

Instructor

To be announced

Reviews

This workshop, amongst the many others is a goldmine! It would be nearly impossible to learn this information any other way. The chance to meet so many talented people, is a great opportunity for later work.
Fall 2017 Student

These workshops bring together physicians and scientists from so many different fields so that knowledge can be shared so easily. Great instruction.

Fall 2017 Student

For this particular session, I really appreciated the background biology information, because it allowed me to contextualize everything more. One recommendation would be to please add a tidbit or two on how to plot.

Fall 2017 Student

Workshop Details

Prerequisites: W1, W2, & W3, or
basic Unix/programming experience
Length: 3 days, 3 hrs per day
Level: Advanced
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Winter 2019 Dates

Will return Spring 2019.