mRNAseq for non-model organisms

Who: Titus Brown (lead instructor); Camille Scott; Tamer Mansour.

When: May 4 and 5, 2015

Times: 9am-3pm on both days

Where: 2030 Valley Hall, UC Davis campus.

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 de novo transcriptome analysis with khmer and Trinity. The primary focus will be on non-model organisms - organisms with no reference genome and poor gene annotations. The workshop will be eukaryote-focused (poly-A mRNA/large genomes/genes with introns).

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

Topics overview

  • Non-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 khmer and Trinity
  • Data analysis & differential expression

The materials for this workshop are available indefinitely here. You might also be interested in the Eel Pond mRNAseq protocol, which lays out a more general protocol for de novo mRNAseq assembly.


  • Mon, 9am-noon: Amazon cloud, read trimming, basic sequence cleaning
  • Mon, noon-1pm: lunch
  • Mon, 1-3pm, assembly
  • Tuesday, 9am-noon: annotation, mapping
  • Tuesday, noon-1pm: lunch
  • Tuesday, 1pm-3pm: quantification and differential expression analysis

Computer 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.

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.