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Lectures
Obi Griffith edited this page Jul 12, 2017
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Presentations:
- Introduction to cloud computing (lecture/tutorial)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
- Introduction to Genome Analysis Platforms (lecture)
- Module 5 - De novo RNA-Seq Assembly and Analysis Using Trinity (lecture)
- Module 6 - Functional Annotation of Assembled Transcripts Using Trinotate (lecture)
Presentations:
- Introduction to cloud computing (lecture/tutorial)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
- Introduction to Genome Analysis Platforms (lecture)
Presentations:
- Introduction to cloud computing (lecture/tutorial)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
- Introduction to Genome Analysis Platforms (lecture)
Presentations:
- Introduction to Cloud Computing (lecture/tutorial)
- [Introduction to Genome Analysis Platforms|LectureFiles/cbw/2016/GenomeAnalysisPlatforms.pdf]]
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
Presentations:
- Introduction to cloud computing (lecture/tutorial)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
Presentations:
- Module 0 - Introduction to cloud computing (lecture/tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
Lecture Videos:
- Module 0 - Introduction to Cloud Computing (lecture)
- Module 1 - Introduction to RNA sequencing and analysis (lecture)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 3 - Expression and Differential Expression (lecture)
- Module 4 - Isoform Discovery and Alternate Expression (lecture)
Presentations:
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
Presentations:
- Module 1 - Introduction to cloud computing (lecture/tutorial)
- Module 2 - Introduction to RNA sequencing (lecture)
- Module 2 - Introduction to RNA sequencing (tutorial)
- Module 3 - RNA-seq alignment and visualization (lecture)
- Module 3 - RNA-seq alignment and visualization (tutorial)
- Module 4 - Expression and differential expression (lecture)
- Module 4 - Expression and differential expression (tutorial)
- Module 5 - Isoform discovery and alternative expression (lecture)
- Module 5 - Isoform discovery and alternative expression (tutorial)
- Introduction to Genome Analysis Platforms
| Previous Section | This Section | Next Section | |:------------------------------------------------------------:|:--------------------------:|:-------------------------------------------:| | Abbreviations | Lectures | Assignment Solutions |
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