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 (BS-Seq). 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 (BS-Seq)
– Pre-processing of BS-Seq 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 is an Associate Researcher in the Department of Molecular, Cell, and Developmental Biology. Dr. Cokus has been doing bioinformatics at UCLA since 2002, and his interests include methods for BS-Seq, RNA-Seq, Hi-C, and protein-protein interaction prediction. His recent work focuses on de novo genome assembly and annotation. Dr. Cokus earned a Ph.D. in Mathematics from the University of Washington.



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: Boyer 529
Seats Available: 28

Fall 2022 Dates

Nov. 15, 16, and 17
1:30 PM – 4:30 PM