Microbial genomics and transcriptomics hands-on, Sep 24-25¶
Who: Ben Johnson (Michigan State University); C. Titus Brown (UC Davis).
Host: C. Titus Brown
When: Sep 24 and 25, 2015
Times: 9am-3pm on both days
Where: Bennett Conference Room, CCAH Facility, 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 host if you are an SVM affiliate.
Description¶
This two-day hands-on workshop will introduce biologists to microbial genomics and transcriptomics. The primary focus will be on genome assembly and annotation, and subsequent transcriptome analysis, of bacteria.
We will be analyzing a stock data set, and we will be using the Amazon cloud.
Topics overview¶
- Logging into the Amazon Cloud
- Short read quality and trimming
- Genome assembly (with SPAdes or MEGAHIT)
- Genome annotation (with Prokka)
- RNAseq analysis
- Differential expression analysis
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