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Authors
- Malachi Griffith1,2,4, mgriffit[AT]genome.wustl.edu, @malachigriffith
- Obi Griffith1,3,4, ogriffit[AT]genome.wustl.edu, @obigriffith
- Jason Walker1, jwalker[AT]genome.wustl.edu
- Ben Ainscough1, bainscou[AT]genome.wustl.edu
- Nicholas Spies1, nspies[AT]genome.wustl.edu
- Alex Wagner1, awagner[AT]genome.wustl.edu, @handlerwagner
- Fouad Yousif5, Fouad.Yousif[AT]oicr.on.ca
1 The Genome Institute, Washington University School of Medicine
2 The Department of Genetics, Washington University School of Medicine
3 The Department of Medicine, Washington University School of Medicine
4 The Siteman Cancer Center, a National Cancer Institute Comprehensive Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine
5 Ontario Institute of Cancer Research
We are grateful to the following people for past and ongoing contributions to this work:
- Francis Ouellette (Ontario Institute for Cancer Research)
- Michelle Brazas (Ontario Institute for Cancer Research)
- Zhibin Lu (Ontario Institute for Cancer Research)
- Rodrigo Goya (British Columbia Cancer Agency)
- Vincent Magrini (McDonnell Genome Institute, Washington University School of Medicine)
- Sean McGrath (McDonnell Genome Institute, Washington University School of Medicine)
- Zachary Skidmore (McDonnell Genome Institute, Washington University School of Medicine)
- Richard K Wilson (McDonnell Genome Institute, Washington University School of Medicine)
- Elaine R Mardis (McDonnell Genome Institute, Washington University School of Medicine)
- All of the students that have taken our RNA-seq courses through CBW or CSHL
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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