A comparative-transcriptomics workshop covering analysis environments, sequence resources, quantification, differential expression, phylogeny, and optional synteny analysis.

Workshop outline

  1. Linux command (bash)/RStudio (R)/Jupyter Notebook (Python)/Evernote (Markdown) Using ChatGPT to write/explain code Github Copilot
  2. Databases: NCBI (USA) /Ensembl (Europe)/ Darwin Tree of Life (UK)
  3. RNA-seq quantification: Mapping and quasi-mapping BLAST/DIAMOND (mapping) Salmon/Kallisto (quasi-mapping)
  4. Differential gene expression Trinity pipeline (DESeq2/EdgeR/Voom) PCA and hierarchical clustering
  5. Phylogeny: OrthoFinder and annotation Orthology assignment (OrthoFinder) Finding single-copy genes (OrthoSNAP) Gene annotation (Swiss-Prot and KEGG) Building tree (IQ-TREE)
  6. Synteny analysis (optional) Microsynteny Macrosynteny
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