Workshop Description

RNA-seq I aims to provide an introduction and the basics tools to process raw RNA-seq data on a cluster machine (Hoffman2). The workshop can serve also as a starting point to develop a gene expression project. This workshop is divided in three days that will cover major steps of processing RNA-seq.

To facilitate learning, the workshop will be centered on hands-on tutorial that will guide students in processing the data from raw reads through read counts using a real case study based approach appropriate for Illumina read data.

RNA-Seq I (taught by Trent Su, Ph.D and Alice Mouton, Ph.D)

From reads to gene expression (raw data processing):

  • Concept of RNA-Seq and experimental design
  • Quality control of RNA-Seq data
  • Mapping RNA-Seq reads to genome
  • Visualization of alignments in genome browsers
  • Quantification of gene expression (gene counts)

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.
  • R:
  • R Studio:
  • We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.


Trent Su, Ph.D., is a postdoctoral fellow at Dr. Siavash Kurdistani lab in the Department of Biological Chemistry. In collaboration with Dr. Arnie Berk lab, his research focus on using high-throughput genomics methods to study genome-wide epigenetic changes induced by Adenoviral oncoprotein e1a which upon expression forces stationary host cells into S phase. Dr. Su received his B.S. in Molecular and Cell Biology at UC Berkeley. Afterwards, he received his M.S. in Computer Science at UC Irvine where he co-written a java web application for Systems Biology pathway modeling. He completed his PhD training in the Kurdistani lab and received his PhD in Oral Biology at UCLA School of Dentistry. His current interests include writing custom python scripts for high-throughput sequencing analysis and mining cancer mutation databases.


Alice Mouton, Ph.D., is an Assistant Project Scientist in Robert Wayne laboratory in the department of Ecology and Evolutionary Biology. Her current researches focus on applying gene expression methodologies (RNA-seq and RRBS) to study non model organisms (bobcat, island fox) in a context of conservation.



Questions addressed by staff very well.
Winter 2018 Student

The slides helped me understand what we were doing with each line line of code.

Fall 2017 Student

Workshop Details

Prerequisites: W1, W2
Recommended: W3
Length: 3 days, 2 hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Spring 2019 Dates

April 30, May 1, and May 2, 2o19
1:30 PM – 3:30 PM