Workshop Description (Intermediate Course)

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.

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)

Workshop Topics

Slides for  RNA-seq I – Day 1

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.


Dr. Lingyun (Ivy) Xiong is a postdoctoral fellow at UCLA, working with Dr. Eric J. Deeds and Dr. Alan Garfinkel’s lab. Ivy focuses on dynamic processes in development, physiology, and cancer, with a special interest in the role of dynamic regulation in health and disease by applying techniques from nonlinear dynamics, computational biology and quantitative imaging. Her research aims to explain the spatiotemporal nature of diverse biological phenomena. Ivy completed her B.Sc. at the University of Hong Kong and earned her D.Phil. from the University of Oxford.

Dr. Karolina E. Kaczor-Urbanowicz, DMD, Phd, MSc is an Assistant Project Scientist in Prof. David Wong’s laboratory of UCLA Center for Oral/Head & Neck Oncology Research and Salivary Diagnostics, Section of Oral Biology, UCLA School of Dentistry. She is a dentist-scientist who graduated from the Faculty of Dental Medicine at the Medical University of Warsaw, Poland. She did her residency in orthodontics simultaneously with the international studies in Bio-Medical Sciences at the Hebrew University of Jerusalem, Israel, working in the Prof. Aaron Palmon’s Laboratory of Proteomics and Salivary Diagnostics, Institute of Dental Sciences. After earning her Ph.D. title, she was awarded the UCLA’s R90 NIH/NIDCR Postdoctoral Dentist-Scientist Scholarship and AACR-DDF postdoctoral fellowship in developing salivary H.pylori exRNA biomarkers for early detection of gastric cancer. At the UCLA, she developed her immense interests in salivary RNA Sequencing, bioinformatics and biomarker development for many oral and systematic diseases including cancer. Email:



Questions addressed by staff very well.

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

Workshop Details

Prerequisites: Intro to Unix (W1), and Using NGS Analysis Tools (W2)
Recommended: Intro to R (W3)
Length: 3 days, 2 hrs per day
Level: Intermediate
Location: Boyer 529
Seats Available: 28

Spring 2024 Dates

May 21, 22, and 23

1:30 PM – 4:30 PM