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.
Description¶
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.
Schedule¶
- 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 http://aws.amazon.com/ before the workshop.
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