1. Introduction 2. Quick Start Virtual Machine 3. Standalone System Requirements 4. Installation, Setup, and Testing a. System Software Pre-requisites b. MAP-RSeq Install c. Post-Install Configuration d. Install validation and test run with example data set 5. Step-by-step instructions to run MAP-RSeq on a user’s sample(s) 6. Using alternate reference sequences 7. Included Bioinformatics Software 8. Limitations to the workflow 9. Post-MAP-RSeq Differential Expression Analysis 10. Contact Information / Support

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