Workshop: mRNAseq

DNA puzzle


April 01 – 9:30 am – 4:30 pm – in person

Prerequisite: Linux Essentials (or proof/assertion of proficiency in bash shell command line.)

REGISTER from calendar on Workshop page.

Note: It is necessary to register for each workshop separately.


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 during the morning session:

  • Quality Control of reads (fastqc)
  • Align reads (bowtie / TopHat)
  • Quantify transcript levels (htseq-count)
  • Differential expression (cuffdiff)
  • Manipulate SAM/BAM files (samtools)
  • Visualization of results (IGV)

Afternoon session will introduce alternate software and dataset.

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: $290 / seat for each student, includes printed materials.

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.