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