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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: The student instructions in Version 4 have been updated to work with current ENSEMBL, Galaxy, and Panther web sites as of June 2021. In addition, one embedded question was removed, and grammatical and mechanical errors were corrected throughout. Read mapping with HISAT2 was included in the PowerPoint presentation.

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