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7-iii. Lectures

Recorded lectures

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)|LectureFiles/cshl/2018/RNASeq_Module0_Introductions.pdf]]
  • [[Module 0 - Introduction to cloud computing (lecture/tutorial)|LectureFiles/cshl/2018/IntroductionToCloudComputing.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (lecture)|LectureFiles/cshl/2018/RNASeq_Module1_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cshl/2018/RNASeq_Module1_Tutorial.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cshl/2018/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cshl/2018/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cshl/2018/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cshl/2018/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Alignment free expression estimation (lecture)|LectureFiles/cshl/2018/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Alignment free expression estimation (tutorial)|LectureFiles/cshl/2018/RNASeq_Module4_Tutorial.pdf]]
  • [[Module 5 - Isoform discovery and alternative expression (lecture)|LectureFiles/cshl/2018/RNASeq_Module5_Lecture.pdf]]
  • [[Module 5 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cshl/2018/RNASeq_Module5_Tutorial.pdf]]
  • [[Module 6/7 - Transcriptome Assembly (lecture)|LectureFiles/cshl/2018/RNASeq_Module6_7_Lecture.pdf]]
  • [[Introduction to IGV Browser (tutorial)|LectureFiles/cshl/2018/IGV_Tutorial_Brief.pdf]]
  • [[Genome Analysis Platforms (lecture)|LectureFiles/cshl/2018/GenomeAnalysisPlatforms.pdf]]

CBW Informatics for RNA-seq analysis (May 28-30, 2018. Toronto, ON, Canada)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

Presentations:

  • [[Intructor Introduction (lecture)|LectureFiles/cbw/2018/RNASeq_Instructor-Introduction.pdf]]
  • [[Module 0 - Introduction to cloud computing (lecture/tutorial)|LectureFiles/cbw/2018/RNASeq_Module0_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (lecture)|LectureFiles/cbw/2018/RNASeq_Module1_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cbw/2018/RNASeq_Module1_Tutorial.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cbw/2018/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cbw/2018/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cbw/2018/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cbw/2018/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Alignment free expression estimation (lecture)|LectureFiles/cbw/2018/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Alignment free expression estimation (tutorial)|LectureFiles/cbw/2018/RNASeq_Module4_Tutorial.pdf]]
  • [[Module 5 - Isoform discovery and alternative expression (lecture)|LectureFiles/cbw/2018/RNASeq_Module5_Lecture.pdf]]
  • [[Module 5 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cbw/2018/RNASeq_Module5_Tutorial.pdf]]
  • [[Module 6 - De novo RNA-Seq assembly and analysis using trinity (lecture)|LectureFiles/cbw/2018/RNASeq_Module6_Lecture.pdf]]
  • [[Module 7 - Functional annotation of assembled transcripts using trinotate (lecture)|LectureFiles/cbw/2018/RNASeq_Module7_Lecture.pdf]]
  • [[Introduction to IGV Browser (tutorial)|LectureFiles/cbw/2018/IGV_Tutorial_Brief.pdf]]

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)|LectureFiles/cshl/2017/IntroductionToCloudComputing.pdf]]
  • [[Introduction to IGV Browser (tutorial)|LectureFiles/cshl/2017/IGV_Tutorial_Brief.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (lecture)|LectureFiles/cshl/2017/RNASeq_Module1_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cshl/2017/RNASeq_Module1_Tutorial.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cshl/2017/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cshl/2017/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cshl/2017/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cshl/2017/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (lecture)|LectureFiles/cshl/2017/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cshl/2017/RNASeq_Module4_Tutorial.pdf]]
  • [[Introduction to Genome Analysis Platforms (lecture)|LectureFiles/cshl/2017/GenomeAnalysisPlatforms.pdf]]

CBW Informatics for RNA-seq analysis (July 10-12, 2017. Toronto, ON, Canada)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

Presentations:

  • [[Introduction to cloud computing (lecture/tutorial)|LectureFiles/cbw/2017/IntroductionToCloudComputing.pdf]]
  • [[Introduction to IGV Browser (tutorial)|LectureFiles/cbw/2017/IGV_Tutorial_Brief.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (lecture)|LectureFiles/cbw/2017/RNASeq_Module1_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cbw/2017/RNASeq_Module1_Tutorial.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cbw/2017/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cbw/2017/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cbw/2017/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cbw/2017/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (lecture)|LectureFiles/cbw/2017/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cbw/2017/RNASeq_Module4_Tutorial.pdf]]
  • [[Introduction to Genome Analysis Platforms (lecture)|LectureFiles/cbw/2017/GenomeAnalysisPlatforms.pdf]]
  • [[Module 5 - De novo RNA-Seq Assembly and Analysis Using Trinity (lecture)|LectureFiles/cbw/2017/RNASeq_Module5_Lecture.pdf]]
  • [[Module 6 - Functional Annotation of Assembled Transcripts Using Trinotate (lecture)|LectureFiles/cbw/2017/RNASeq_Module6_Lecture.pdf]]

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)|LectureFiles/cbw-cshl/2017/IntroductionToCloudComputing.pdf]]
  • [[Introduction to IGV Browser (tutorial)|LectureFiles/cbw-cshl/2017/IGV_Tutorial_Brief.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (lecture)|LectureFiles/cbw-cshl/2017/RNASeq_Module1_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cbw-cshl/2017/RNASeq_Module1_Tutorial.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cbw-cshl/2017/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cbw-cshl/2017/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cbw-cshl/2017/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cbw-cshl/2017/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (lecture)|LectureFiles/cbw-cshl/2017/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cbw-cshl/2017/RNASeq_Module4_Tutorial.pdf]]
  • [[Introduction to Genome Analysis Platforms (lecture)|LectureFiles/cbw-cshl/2017/GenomeAnalysisPlatforms.pdf]]

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)|LectureFiles/cshl/2016/IntroductionToCloudComputing.pdf]]
  • [[Introduction to IGV Browser (tutorial)|LectureFiles/cshl/2016/IGV_Tutorial_Brief.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (lecture)|LectureFiles/cshl/2016/RNASeq_Module1_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cshl/2016/RNASeq_Module1_Tutorial.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cshl/2016/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cshl/2016/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cshl/2016/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cshl/2016/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (lecture)|LectureFiles/cshl/2016/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cshl/2016/RNASeq_Module4_Tutorial.pdf]]
  • [[Introduction to Genome Analysis Platforms (lecture)|LectureFiles/cshl/2016/GenomeAnalysisPlatforms.pdf]]

CBW Informatics for RNA-seq analysis (June 16-17, 2016. Toronto, ON, Canada)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

Videos of lectures (Youtube)

Presentations:

  • [[Introduction to Cloud Computing (lecture/tutorial)|LectureFiles/cbw/2016/RNASeq_Module0_Lecture.pdf]]
  • [Introduction to Genome Analysis Platforms|LectureFiles/cbw/2016/GenomeAnalysisPlatforms.pdf]]
  • [[Introduction to IGV Browser (tutorial)|LectureFiles/cbw/2016/IGV_Tutorial_Brief.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (lecture)|LectureFiles/cbw/2016/RNASeq_Module1_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cbw/2016/RNASeq_Module1_Tutorial.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cbw/2016/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cbw/2016/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cbw/2016/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cbw/2016/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (lecture)|LectureFiles/cbw/2016/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cbw/2016/RNASeq_Module4_Tutorial.pdf]]

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)|LectureFiles/cshl/2015/IntroductionToCloudComputing.pdf]]
  • [[Introduction to IGV Browser (tutorial)|LectureFiles/cshl/2015/IGV_Tutorial_Brief.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (lecture)|LectureFiles/cshl/2015/RNASeq_Module1_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cshl/2015/RNASeq_Module1_Tutorial.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cshl/2015/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cshl/2015/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cshl/2015/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cshl/2015/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (lecture)|LectureFiles/cshl/2015/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cshl/2015/RNASeq_Module4_Tutorial.pdf]]

CBW Informatics for RNA-seq analysis (June 8-9, 2015. Toronto, ON, Canada)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

Presentations:

  • [[Module 0 - Introduction to cloud computing (lecture/tutorial)|LectureFiles/cbw/2015/RNASeq_Module0_AmazonPreTutorial.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (lecture)|LectureFiles/cbw/2015/RNASeq_Module1_Lecture.pdf]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cbw/2015/RNASeq_Module1_Tutorial.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cbw/2015/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cbw/2015/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cbw/2015/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cbw/2015/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (lecture)|LectureFiles/cbw/2015/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cbw/2015/RNASeq_Module4_Tutorial.pdf]]

Lecture Videos:

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)|LectureFiles/cbw-cshl-nygc/2015/RNASeq_Module1_Lecture.pptx]]
  • [[Module 1 - Introduction to RNA sequencing (tutorial)|LectureFiles/cbw-cshl-nygc/2015/RNASeq_Module1_Tutorial.pptx]]
  • [[Module 2 - RNA-seq alignment and visualization (lecture)|LectureFiles/cbw-cshl-nygc/2015/RNASeq_Module2_Lecture.pptx]]
  • [[Module 2 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cbw-cshl-nygc/2015/RNASeq_Module2_Tutorial.pptx]]
  • [[Module 3 - Expression and differential expression (lecture)|LectureFiles/cbw-cshl-nygc/2015/RNASeq_Module3_Lecture.pptx]]
  • [[Module 3 - Expression and differential expression (tutorial)|LectureFiles/cbw-cshl-nygc/2015/RNASeq_Module3_Tutorial.pptx]]
  • [[Module 4 - Isoform discovery and alternative expression (lecture)|LectureFiles/cbw-cshl-nygc/2015/RNASeq_Module4_Lecture.pptx]]
  • [[Module 4 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cbw-cshl-nygc/2015/RNASeq_Module4_Tutorial.pptx]]

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)|LectureFiles/cshl/2014/RNASeq_Module1_AmazonPreTutorial.pdf]]
  • [[Module 2 - Introduction to RNA sequencing (lecture)|LectureFiles/cshl/2014/RNASeq_Module2_Lecture.pdf]]
  • [[Module 2 - Introduction to RNA sequencing (tutorial)|LectureFiles/cshl/2014/RNASeq_Module2_Tutorial.pdf]]
  • [[Module 3 - RNA-seq alignment and visualization (lecture)|LectureFiles/cshl/2014/RNASeq_Module3_Lecture.pdf]]
  • [[Module 3 - RNA-seq alignment and visualization (tutorial)|LectureFiles/cshl/2014/RNASeq_Module3_Tutorial.pdf]]
  • [[Module 4 - Expression and differential expression (lecture)|LectureFiles/cshl/2014/RNASeq_Module4_Lecture.pdf]]
  • [[Module 4 - Expression and differential expression (tutorial)|LectureFiles/cshl/2014/RNASeq_Module4_Tutorial.pdf]]
  • [[Module 5 - Isoform discovery and alternative expression (lecture)|LectureFiles/cshl/2014/RNASeq_Module5_Lecture.pdf]]
  • [[Module 5 - Isoform discovery and alternative expression (tutorial)|LectureFiles/cshl/2014/RNASeq_Module5_Tutorial.pdf]]
  • [[Introduction to Genome Analysis Platforms|LectureFiles/cshl/2014/GenomeAnalysisPlatforms.pdf]]

CBW Informatics for RNA-seq analysis (June 19-20, 2014. Vancouver, BC, Canada)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

CBW Informatics for RNA-seq analysis (June 2-3, 2014. Montreal, QC, Canada)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

CBW Informatics for RNA-seq analysis (June 3-4, 2013. Toronto, ON, Canada)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

CBW Informatics on High Throughput Sequencing Data (June 11-12, 2012. Toronto, ON, Canada)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

[[Previous Section|Abbreviations]] [[This Section|Lectures]] [[Next Section|Solutions]]
[[Abbreviations|Abbreviations]] [[Lectures|Lectures]] [[Assignment Solutions|Solutions]]