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RNAseq data analysis using Galaxy

Author(s): Matthew Escobar1, Sam S Donovan2, Irina Makarevitch3, Bill Morgan4, Sabrina Robertson5

1. California State University San Marcos 2. University of Pittsburgh 3. Hamline University 4. The College of Wooster 5. North Carolina State University

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This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.


This resource involves downloading RNAseq data sets from the NCBI Sequence Read Archive (SRA) and using Galaxy tools to identify differentially expressed genes. Different data sets and experimental questions can be explored. Students are introduced to all major computational steps in RNAseq data analysis, including the concept of computational pipelines/workflows.


Revisions to previous version: In addition to minor clarification of the tutorial instructions, embedded questions were added to prompt student engagement and reflection. The grading key for tutorial questions was correspondingly updated. The PowerPoint presentation was revised to include flow diagrams of the overall procedure. Finally, the Instructor Background document was significantly revised; most notably the section on alternative RNA-seq data sets was expanded to suggest additional options. 

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