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 Materials

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. Arjun Bhattacharya is a Postdoctoral Fellow in the Department of Pathology and Laboratory Medicine with Prof. Bogdan Pasaniuc and Prof. Michael Gandal. Arjun’s research focuses on integrative methods for statistical genetics and genetic epidemiology to study complex traits, mainly cancer, neuropsychiatric disorders, and neonatal traits. He received his BS in Biology and Statistics at the University of North Carolina at Chapel Hill and a PhD in Biostatistics at the Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Email:

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: W1, W2
Recommended: W3
Length: 3 days, 2 hrs per day
Level: Intermediate
Location: Boyer 529
Seats Available: 28

Spring 2023 Dates

May 23, 24, and 25

1:30 PM – 4:30 PM