SYLLABUS

Transcriptome Assembly, Differential Expression, and Gene Annotation

Main topics:

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• Experimental design

• Tools for RNA-seq data analysis and quality control

• Transcriptome assembly

• Normalization and differential expression analysis

• Splicing analysis and multiple testing

• Biological interpretation

• Introduction to gene annotation

• Ab initio gene annotation

• Homology-based gene annotation

• Visualizing gene annotation

• Sharing gene annotation

• Managing data from public databases

Also, if time allows, we will briefly discuss other analyses of RNA-seq results (e.g., qPCR, transformation) and examples of functional analysis beyond gene annotation (e.g., pathway analyses; KEGG, Pathview).