Skip to main content
University of Wisconsin–Madison

Bioinformatics Resource Center

The UW Biotechnology Center is following University guidelines regarding COVID-19.

We understand how this disruption of service has impacted your research and we are continuing essential projects.

mRNAseq Data Analysis Workshop

2020 date(s):
Monday, February 28 -  9am - 4:30pm

: Linux Essentials workshop (or proof/assertion of proficiency in bash shell)

Location: Genetics/Biotech Center
425 Henry Mall Madison, WI 53706 

LIMITED to 10  participants - (2 minimum)

REGISTER: use Google Calendar link to register on chosen date
It is necessary to register for each workshop separately.
- Printed original exercise book: 
if registration is less than 1 week a photocopy version may be substituted.


The workshops will focus on introducing researchers to the principles behind RNA-Seq analysis and will provide a hands-on introduction to software and analysis pipelines for RNA-Seq. Workshop is aimed at teaching the computational process that takes the raw data all the way through the high level analysis. We will focus on advanced analysis using a Linux command line environment to run open-source RNA-Seq software in this all day workshop with lecture and hands on exercises. The morning session has more "hand holding" and the afternoon session provides time for applying what was learned.

Materials will cover the following topics:

  • Quality Control of reads
  • Align reads
  • Quantify transcript levels
  • Differential expression
  • Manipulate SAM/BAM files

Participants are expected to have a basic knowledge of the Linux environment (bash shell) and a basic understanding of statistical methods.


Must be comfortable with the Linux command line and familiar with basic Linux commands. 

If you have registered for the Linux Basic for NGS Data Analysis you are considered to meet the prerequisite.

* There is a minimal set of software that should be installed on laptops BEFORE attending the workshop. Instructions will be provided to attendees prior to the workshop and can be found within the PDF document: Preparation for Linux-based worshop  

Fee: $190 / seat

Jean-Yves Sgro,  Ph.D., Biotechnology Center -

Previous instructor(s):
Dr. Deborah Muganda-Rippchen, Ph.D. Center for Predictive Computational Phenotyping
Dr. Jeremy Glasner, Ph.D.,  Biotechnology Center

*No-show Policy*
All cancellations need to be notified 72 hours in advance.