Module-00-Setup

• Introduction to RNA-seq and course setup

• Citation

• Syntax

• Laptop setup instructions

• Prerequisites

• Introduction to AWS

• Log into AWS

• Unix

• Environment

• Tool Installation

---

Module-01-Inputs

• Introduction to Inputs

• Reference Genomes

• Annotations

• Indexing

• RNAseq Data

• Pre-alignment QC

---

Module-02-Alignment

• Introduction to Alignment

• Adapter Trim

• Alignment

• IGV

• Alignment Visualization

• Alignment QC

---

Module-03-Expression

• Introduction to Expression Analysis

• Expression

• Differential Expression

• Ballgown DE Visualization

• Batch Correction

• DE Pathway Analysis

---

Module-04-Kallisto

• Introduction to Alignment Free Analysis

• Alignment Free Expression Estimation (Kallisto)

---

Module-05-Isoforms

• Introduction to Isoform Analysis

• Reference Guided Transcript Assembly

• De Novo Transcript Assembly

• Transcript Assembly Merge

• Differential Splicing

• Transcript Assembly Visualization

---

Module-06-Trinity

• Introduction to De Novo Assembly

• Trinity

---

Module-07-Trinotate

• Introduction to Transcript Annotation

• Trinotate

---

Module-08-scRNA

• Introduction to Single-cell RNA-seq

• Single-cell RNA-seq

---

Module-09-Appendix

• Introduction to the Appendix

• Saving Results

• Abbreviations

• Lectures

• Practical Exercise Solutions

• Team Assignment - Alignment

• Team Assignment - Expression and DE

• Integrated Assignment

• Integrated Assignment Answers

• AWS Setup

• Bioinformatics Best Practices

• Complete Result Sets

• Strand Settings

• Log into Compute Canada