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

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.


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