Galaxy Community Conference 2016 (GCC16)

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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.

• An alternative RNAseq analysis pipeline using count based quantification methods (DESeq2, edgeR, or limma) to generate abundance measurements.

These three pipelines would be used as examples to highlight usage of workflows and their advanced features.

Prerequisites: 

• A general knowledge of Galaxy (for example, you should be familiar with the material in Galaxy 101 or have attended Introduction to Galaxy).

• A wi-fi enabled laptop with a modern web browser.  Google Chrome, Firefox and Safari will work best.