Workshop: mRNAseq – Tuxedo Suite 2

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2024 date(s)

April 8 – 9:30 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.

Description

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 uses bowtie, TopHat, Cuffdiff.)

Materials will cover the following topics:

  • Quality Control of reads (fastqc, multiqc)
  • Align reads (HiSat2)
  • Quantify transcript levels (StringTie)
  • Differential expression (StringTie/Ballgown)
  • Manipulate SAM/BAM files (samtools)
  • Visualization of results (IGV, Ballgown)

We will run an analysis from data small enough for a Desktop/laptop computer with modern hardware (see requirements) with a method suitable for Macintosh, Windows, and Linux (including Windows WSL Linux) that can be scaled to larger computers such as a Linux server.

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

Instructor(s):
Dr. Jean-Yves Sgro,  Ph.D., Biotechnology Center – jsgro@wisc.edu

Previous instructor(s):
None.

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