Workshop Description (Intermediate Course)

Almost all Illumina high-throughput sequencing today involves multiplexing of samples within lanes. High selectivity and sensitivity of the necessitated post-sequencing demultiplexing is important for experimental success. However, there are several under-appreciated/surprising aspects of multiplexing on the Illumina platform, and common analysis workflows do not provide strong signals of all problems at this level, leading to a widespread impression that demultiplexing is a trivial topic, when it is not. This workshop will discuss multiplexing on the Illumina platform (including single and dual indices, unique duals, and UMIs), use of the Illumina BCL2FASTQ2 tool (on the campus Hoffman2 cluster), and QC steps (via command line tools) that should be considered for all experiments (even if you typically rely on a Core’s nominal demultiplexing). A focus will be on specific classes of problems actually observed by the Instructor’s demultiplexing without typical assumptions of more than 600 diverse NovaSeq lanes from the full spectrum of BSCRC Sequencing Core users.

Workshop Materials


  • TBA
  • TBA

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.


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 Command Line), W2 (Using NGS Analysis Tools), and W16 (Library Prep for NGS) is recommended, but not required.
Length: 3 days, 3 hrs per day
Level: Intermediate
Location: Boyer 529
Seats Available: 28

Winter 2023 Dates

Feb 28, Mar. 1 and Mar. 2
9:00 AM – 12:00 PM