Transcriptomics

• Considerations for reference vs reference-free transcriptome analysis
  • Reference-based transcriptome analysis
  • Reference-free transcriptome analysis
• RNA-seq and Differential Gene Expression in Bacteria
  • Learning goals
  • Additional Resource - Basic Linux/Unix commands
• Setting up your RNA-seq project
  • Start a virtual notebook
• Quality control and trimming of reads
  • Trimmomatic
  • FastQC
• Align and count gene features
  • Align the trimmed reads with Bowtie
  • Count gene features/quantify transcript abundance with HTSeq
• Differential gene expression
  • Using an available workflow that links all of these steps together
  • Identifying batch effects
  • Underlying assumptions (worth knowing) of differential gene expression packages (edgeR and DESeq)

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