2015 / September / Microbial genomics and transcriptomics

This workshop was given on Sep 24th and 25th, 2015, by C. Titus Brown and Ben Johnson. See the workshop organization page for more information, or contact Titus directly.

• Welcome!
  • 1. Learning goals
  • 2. Safe space and code of conduct
  • 3. Instructor introductions
  • 4. Amazon and cloud computing - why?!
  • 5. Sticky notes and how they work... + Minute Cards
  • 6. Warning:
• Getting started with Amazon EC2
  • Start up an EC2 instance
  • Logging into your new instance “in the cloud” (Windows version)
  • Logging into your new instance “in the cloud” (Mac version)
  • Terminating your instance
  • Amazon Web Services reference material
• Genomics
  • Short read quality and trimming
  • Assembling E. coli sequences with SPAdes
  • Bacterial genome annotation using Prokka
• Transcriptomics
  • Considerations for reference vs reference-free transcriptome analysis
  • RNA-seq and Differential Gene Expression in Bacteria
  • Setting up your RNA-seq project
  • Quality control and trimming of reads
  • Align and count gene features
  • Differential gene expression

Indices and tables

• Index
• Module Index
• Search Page

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