Workshop: Transcript-level mRNAseq on the desktop with Docker



July 12 – 9:00 am – 4:30 pm – in person

Prerequisite: Linux Essentials (or proof/assertion of proficiency in bash shell. Some R experience useful but not mandatory.)

REGISTER from calendar on Workshop page.

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


This (all day) new workshop will explore the Tuxedo Suite #2 (Hisat2, StringTie, and R-based package Ballgown)  to analyze transcript-level analysis of bulk mRNA-seq experiments including differential gene expression. (Older Tuxedo Suite # 1 concits of bowtie/TopHat, Cuffdiff.)

We will run an analysis from data small enough for a Dektop/laptop computer with modern hardware (see requirements) and explore the “container” methods to use a Macintosh or a Windows computer to run Linux-bsaed software thanks for containers (with Docker Desktop.)

As such this workshop is as much a Next Gen Data analysis training as it is a Bioinformtics training that can be scaled to larger computers.

Hardware Requirements: A laptop following the University suggestions for students should be adequate for this workshop. See Computers & equipment for students: what do I need? However, a computer with 16 Gb RAM rather than 8 Gb would be more appropriate.

Prior training: Students should be familiar with the concept of “command line” typed within a terminal. The “Linux Essentials” workshop would be helpful. Macintosh users will use a Terminal with bash or with zsh while Windows users will run from a PowerShell Terminal. These are “built-in” the operating systems and do not need installation.

A the latter portion of the workshop is carried within R and RStudio. Familiarity with these systems would be useful.

The workshop consists of short lecture material with emphasis on active hands-on exercises.

A $375 fee is required for each participants that includes printed materials.

* 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

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

Previous instructor(s):

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