Workshop Description (Intermediate Course)

This workshop will introduce the basic principles of DNA methylation and briefly describe available methods for DNA methylation assessment, focusing on bisulfite sequencing (BSseq). We will cover the principles of BSseq preprocessing, alignment and methylation calling, differential methylation analysis, annotation and visualization. Attendees will  have the opportunity to work on real DNA methylation data provided by the instructor and run the analysis on Hoffman2 and locally. Attendees need to have a basic knowledge in UNIX commands and R programming for this workshop. No previous experience with NGS or DNA methylation analysis is necessary. 

Workshop Materials

– Intro to DNA methylation and Bisulfite Sequencing (BSseq)
– Pre-processing of BSseq data
– Alignment

– Methylation calling and matrices
– Differential methylation and annotation

– Differential methylation and variability, annotation, visualization

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.
  • It is recommended for attendees to have R ( ( installed locally (on their own laptop).


Dr. Shawn Cokus



Workshop Details

Prerequisites: W1 (Intro to UNIX) and W3 (Intro to R) or equivalent experience with UNIX and R programming.   Recommended: W2 (Using NGS Analysis tools)

Length: 3 days, 3 hrs per day
Level: Intermediate
Location: ZOOM
Seats Available: TBD

Winter 2021 Dates

February 23, 24, and 25
9:00 AM to 12:00 PM