Module-00-Setup
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Introduction to RNA-seq and course setup
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Citation
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Syntax
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Laptop setup instructions
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Prerequisites
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Introduction to AWS
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Log into AWS
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Unix
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Environment
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Tool Installation
Module-01-Inputs
Module-02-Alignment
Module-03-Expression
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Introduction to Expression Analysis
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Expression
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Differential Expression
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Ballgown DE Visualization
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Batch Correction
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DE Pathway Analysis
Module-04-Kallisto
Module-05-Isoforms
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Introduction to Isoform Analysis
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Reference Guided Transcript Assembly
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De Novo Transcript Assembly
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Transcript Assembly Merge
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Differential Splicing
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Transcript Assembly Visualization
Module-06-Trinity
Module-07-Trinotate
Module-08-scRNA
Module-09-Appendix
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Introduction to the Appendix
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Saving Results
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Abbreviations
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Lectures
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Practical Exercise Solutions
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Team Assignment - Alignment
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Team Assignment - Expression and DE
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Integrated Assignment
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Integrated Assignment Answers
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AWS Setup
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Bioinformatics Best Practices
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Complete Result Sets
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Strand Settings
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Log into Compute Canada