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Obi Griffith edited this page Jul 11, 2017 · 78 revisions

Informatics for RNA-seq: A web resource for analysis on the cloud

Welcome to the RNA-seq Tutorial. Use this page to navigate your way through all exercises. Each page has a link at the bottom to bring you back to this table of contents. A version of this tutorial was accompanied by a publication. If you find the materials here or in that paper useful, please cite the following:

Malachi Griffith*, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith*. 2015. Informatics for RNA-seq: A web resource for analysis on the cloud. PLoS Comp Biol. 11(8):e1004393.

*To whom correspondence should be addressed: E-mail: mgriffit[AT]genome.wustl.edu, ogriffit[AT]genome.wustl.edu

Note: An archived version of this tutorial exists here. This version is maintained for consistency with the published materials (Griffith et al. 2015. PLoS Comp Biol.) and for past students wishing to review covered material. However, we strongly suggest that you continue with the current version of the tutorial below.

Table of Contents

  1. Module 0 - Introduction and Cloud Computing
    1. Authors
    2. Citation and Supplementary Materials
    3. Syntax
    4. Intro to AWS Cloud Computing
    5. Logging into Amazon Cloud
    6. Unix Bootcamp
    7. Environment
    8. Resources
  2. Module 1 - Introduction to RNA sequencing
    1. Installation
    2. Reference Genome
    3. Annotation
    4. Indexing
    5. RNA-seq Data
    6. PreAlignment QC
  3. Module 2 - RNA-seq Alignment and Visualization
    1. Preprocessing
    2. Alignment
    3. IGV
    4. PostAlignment Visualization
    5. PostAlignment QC
  4. Module 3 - Expression and Differential Expression
    1. Expression
    2. Differential Expression
    3. DE Visualization
    4. Kallisto for Reference Free Abundance Estimation
  5. Module 4 - Isoform Discovery and Alternative Expression
    1. Reference Guided Transcript Assembly
    2. de novo Transcript Assembly
    3. Transcript Assembly Merge
    4. Differential Splicing
    5. Transcript Assembly Visualization
  6. Module 5 - Trinity Assembly And Analysis
    1. Trinity Assembly And Analysis
  7. Module 6 - Trinotate Functional Annotation
    1. Trinotate Functional Annotation
  8. Appendix
    1. Abbreviations
    2. Lectures
    3. Practical Exercise Solutions
    4. Integrated Assignment
    5. Proposed Improvements
    6. AWS Setup

NOTICE: This resource has been moved to rnabio.org. The version here will be maintained for legacy use only. All future development and maintenance will occur only at rnabio.org. Please proceed to rnabio.org for the current version of this course.

Table of Contents
Module 0: Authors | Citation | Syntax | Intro to AWS | Log into AWS | Unix | Environment | Resources
Module 1: Installation | Reference Genomes | Annotations | Indexing | Data | Data QC
Module 2: Adapter Trim | Alignment | IGV | Alignment Visualization | Alignment QC
Module 3: Expression | Differential Expression | DE Visualization
Module 4: Alignment Free - Kallisto
Module 5: Ref Guided | De novo | Merging | Differential Splicing | Splicing Visualization
Module 6: Trinity
Module 7: Trinotate
Appendix: Saving Results | Abbreviations | Lectures | Practical Exercise Solutions | Integrated Assignment | Proposed Improvements | AWS Setup

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