This workshop would cover standard, advanced, and alternative RNAseq analysis pipelines, all using workflows and highlighting their advanced features. Three general pipelines would be addressed:
A standard RNAseq analysis pipeline using the Tuxedo suite (Tophat → Cuffdiff) for standard transcript quantification with a reference transcriptome.
An advanced analysis pipeline using the Tuxedo suite with StringTie to create de novo transcript structures, merge these with reference transcripts to create a transcripteome database, followed by transcript quantification.
These three pipelines would be used as examples to highlight usage of workflows and their advanced features.