Module-00-Setup

• Introduction to RNA-seq and course setup

• Citation

• Syntax

• Introduction to AWS

• Log into AWS

• Unix

• Environment

• Tool Installation

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Module-01-Inputs

• Introduction to Inputs

• Reference Genomes

• Annotations

• Indexing

• RNAseq Data

• Pre-alignment QC

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Module-02-Alignment

• Introduction to Alignment

• Adaptor Trim

• Alignment

• Alignment Visualization

• Alignment QC

• IGV

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Module-03-Expression

• Introduction to Expression Analysis

• Expression

• Differential Expression

• Ballgown DE Visualization

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Module-04-Kallisto

• Introduction to Alignment Free Analysis

• Alignment Free Expression Estimation (Kallisto)

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Module-05-Isoforms

• Introduction to Isoform Analysis

• Reference Guided Transcript Assembly

• De Novo Transcript Assembly

• Transcript Assembly Merge

• Differential Splicing

• Transcript Assembly Visualization

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Module-06-Trinity

• Introduction to De Novo Assembly

• De novo RNA-Seq Assembly and Analysis

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Module-07-Trinotate

• Introduction to Transcript Annotation

• Trinotate

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Module-08-Appendix

• Introduction to the Appendix

• Saving Results

• Abbreviations

• Lectures

• Practical Exercise Solutions

• Integrated Assignment

• Integrated Assignment Answers

• Proposed Improvements

• AWS Setup

• Bioinformatics Best Practices