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Welcome to the wiki for RNA-Seq Tutorials brought to you by the University of Miami's Center for Computational Science Student Mentors! We hope that this wiki (and the accompanying scripts in the github repository) will be a helpful guide to you as you embark on the journey of analyzing an RNA-Seq data set!

Please note that these tutorials assume you already have a basic handle on unix/linux.

1. Module 1 - Preparations
1. Authors of these tutorials
2. How to cite these tutorials
3. Suggested Folder Organization
4. Finding your input FastQ Files
5. Loading the FastQ Files onto the server
2. Module 2 - Aligning Reads to the Genome
1. Tophat
1. Preparing to use Tophat
2. Running Tophat
2. STAR
1. Preparing to use STAR
2. Running STAR
3. Quality Checking
1. Coming Soon!
4. Where do I go from here? Gene-level vs Isoform-level analysis
3. Module 3 - Gene Level Analysis
1. Introduction to Gene Level Analysis
2. Sorting Aligned Reads
3. Counting Reads over Gene Intervals
4. Differential Expression Analysis
1. DESeq2
1. Preparing to run DESeq2
2. Simple DESeq2 Analysis
3. Simple DESeq2 Analysis using Gene Names
4. DESeq2 Analysis with Multiple Variables
2. EdgeR
1. Preparing to run EdgeR
2. Simple EdgeR Analysis
3. EdgeR Analysis with Multiple Variables
4. Module 4 - Isoform Level Analysis
1. Coming Soon!