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.
Description¶
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.
Schedule¶
- 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
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