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Lectures
Obi Griffith edited this page Nov 14, 2018
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2016 CBW course lectures (YouTube)
CSHL Advanced Sequencing Technologies and Applications (November 6-18, 2018. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Instructor Introduction (lecture)
- 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 - Alignment free expression estimation (lecture)
- Module 4 - Alignment free expression estimation (tutorial)
- Module 5 - Isoform discovery and alternative expression (lecture)
- Module 5 - Isoform discovery and alternative expression (tutorial)
- Module 6/7 - Transcriptome Assembly (lecture)
- Introduction to IGV Browser (tutorial)
- Genome Analysis Platforms (lecture)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Intructor Introduction (lecture)
- 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 - Alignment free expression estimation (lecture)
- Module 4 - Alignment free expression estimation (tutorial)
- Module 5 - Isoform discovery and alternative expression (lecture)
- Module 5 - Isoform discovery and alternative expression (tutorial)
- Module 6 - De novo RNA-Seq assembly and analysis using trinity (lecture)
- Module 7 - Functional annotation of assembled transcripts using trinotate (lecture)
- Introduction to IGV Browser (tutorial)
CSHL Advanced Sequencing Technologies and Applications (November 7-18, 2017. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
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)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
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)
CBW-CSHL High-Throughput Biology: From Sequence to Networks (March 20-26, 2017. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) and Canadian Bioinformatics Workshops (CBW) - Course Site
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)
CSHL Advanced Sequencing Technologies and Applications (November 7-20, 2016. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
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)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Videos of lectures (Youtube)
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)
CSHL Advanced Sequencing Technologies and Applications (November 10-22, 2015. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
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)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
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)
CSHL-CBW-NYGC High-throughput Biology: From Sequence to Networks (April 29-30, 2015. New York, NY, USA)
Organized by New York Genome Center (NYGC), Canadian Bioinformatics Workshops (CSHL), and Cold Spring Harbor Laboratory (CSHL) - Course Site
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)
CSHL Advanced Sequencing Technologies and Applications (November 11-23, 2014. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
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
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
| 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