mRNAseq for semi-model organisms

Who: Titus Brown (lead instructor); Dr. Isabelle Laforest-Lapointe; Dr. Tamer Mansour.

When: March 4 and 5, 2015

Times: 9am-3pm on both days

Where: Valley Hall, UC Davis campus. Day 1: 2030 Valley; Day 2: 1041 Valley.

Cost: there is no fee.

This workshop is open to everyone, including graduate students, postdocs, staff, faculty, and community members. We have extra space for UC Davis VetMed affiliates; contact the lead instructor if you are an SVM affiliate.


This two-day hands-on workshop will introduce biologists to doing reference-based transcriptome analysis with TopHat, Cufflinks, and DAVID. The primary focus will be on “semi-model” organisms - organisms with good quality reference genomes but relatively incomplete gene annotations. This includes most animals and plants that are not a major model organism. The workshop will be eukaryote-focused (large genomes, and genes with introns).

We will be analyzing a stock data set, and we will be using the Amazon cloud.

Topics overview

  • Semi-model organisms and RNAseq: an overview of the options
  • Logging into the Amazon Cloud
  • Short read quality and trimming
  • Building a new reference transcriptome with TopHat and Cufflinks
  • Mapping reads to the transcriptome with TopHat
  • Processing another sample with TopHat and HTSeq
  • Data analysis & differential expression

The materials for this workshop are available indefinitely here.


  • Wed, 9am-noon: Amazon cloud, read trimming, basic sequence cleaning
  • Wed, noon-1pm: lunch
  • Wed, 1-3pm, building gene models
  • Thursday, 9am-noon: mapping, quantification
  • Thursday, noon-1pm: lunch
  • Thursday, 1pm-3pm: differential expression analysis

Computer and workshop requirements

Attendees will need to bring a computer with a Web browser, an Internet connection, and an ssh client; Windows users should install MobaXterm before the workshop.

Please sign up for an account at before the workshop.

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.