Lectures

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Recorded lectures

• 2021 CSHL course lectues (WUSTL Box)
• 2020 CSHL course lectures (WUSTL Box)
• 2018 CBW course lectures (YouTube)
• 2016 CBW course lectures (YouTube)
• 2015 CBW course lectures (YouTube)
• 2014 CBW course lectures (YouTube)
• 2013 CBW course lectures (YouTube)

CBW RNA-seq analysis (July 17-19th, 2023. Toronto, ON, Canada))

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

Presentations:

• Intructor Introductions
• Introduction to Cloud Computing (lecture)
• Introduction to RNA Sequencing (lecture)
• Introduction to IGV (lecture)
• Fasta, Fastq, GTF (mini lecture)
• Indexing (mini lecture)
• Alignment (mini lecture)
• Alignment, assembly, kmers (mini lecture)
• SAM, BAM, BED (mini lecture)
• Alignment QC (mini lecture)
• Abundance Estimation (mini lecture)
• HTSeq (mini lecture)
• Differential expression (mini lecture)
• Alignment free analysis with Kallisto (mini lecture)
• Alternative expression (mini lecture)

Advanced Sequencing Technologies & Bioinformatics Analysis (November 7-19, 2022)

Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site

Presentations:

• Overview of Next-generation Short Read Sequencing Technologies (Elaine Mardis)
• Emerging next-generation sequencing platforms (Elaine Mardis)
• ChIP and Epigenomics (Berkley Gryder)
• Research Applications of Single Cell Sequencing (Trevor Pugh)
• Long read sequencing technology and research applications (Richard McCombie)
• Single cell sequencing technology and applications (Jonathan Preall)
• Computational Biology at the New York Genome Center (Mike Zody)
• An Overview of Bioinformatics (Chris Miller)
• Introduction to Cloud Computing (Kelsy Cotto)
• File formats (Felicia Gomez)
• Alignment concepts (Felicia Gomez)
• Introduction to IGV (My Hoang)
• Introduction to epigenomics - ATAC, ChIPseq and Bisulfite approaches (Chris Miller)
• Introduction to bulk RNA-sequencing(Malachi Griffith)
• Noncoding RNAs (Chris Maher)
• Introduction to scRNA analysis (Jonathan Preall)
• scRNA analysis notebook (Jonathan Preall)
• Bedtools Introduction (Jason Kunisaki)
• Genomic arithmetic with bedtools (Aaron Quinlan)
• Real world analysis with bedtools (Aaron Quinlan)
• SNP and indel discover (Joshua Mincer)
• Computational Challenges in Rare Disease Analysis (Aaron Quinlan)
• Variant Representation and Interpretation (Alex Wagner)
• Working with clusters, shell profiles, Unix extras
• Central Limit Theorum (Aaron Quinlan)
• t-stat, t-distribution, t-tests, and p-values (Aaron Quinlan)
• The T2T Genome and applications to variant calling (Dylan Taylor)

Advanced Sequencing Technologies & Bioinformatics Analysis (November 11-19, 2021. Virtual due to COVID-19)

Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site

Presentations:

• Next Generation Sequencing (Short Read) Technologies (Elaine Mardis)
• Long Read Sequencing (Dick McCombie)
• Population sequencing and analysis projects at NYGC (Mike Zody)
• Single Cell Sequencing (Jonathan Preall)
• Introduction to Cloud Computing (Obi Griffith)
• A Brief Intro to the Human Genome and FASTA (Aaron Quinlan)
• A Brief Intro to FASTQ format (Aaron Quinlan)
• DNA sequence mapping and alignment (Aaron Quinlan)
• SAM/BAM format, samtools, and IGV-ish (Aaron Quinlan)
• Brief Intro SNV Discovery (Aaron Quinlan)
• Intro to RNA-sequencing and analysis (Malachi Griffith)
• A complete reference genome improves analysis of human genetic variation (Michael Schatz)
• Analysis and interpretation of single-cell RNA-seq data (Chris Miller)
• Variant Representation, Annotation, and Interpretation (Alex Wagner)
• Metagenomics and Viromics (Scott Handley)
• Multiome experiment (Jonathan Preall)
• Comprehensive Analysis of Single Cell Epigenomic Data (Yang Li)
• The application of epigenomic profiling strategies to study cancer and other common diseases (Peter Scacheri)

CBW RNA-seq analysis (September 8-10th, 2021. VIRTUAL due to COVID-19)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

Presentations:

• Intructor Introductions
• Introduction to RNA Sequencing (lecture)
• Introduction to IGV (lecture)
• Fasta, Fastq, GTF (mini lecture)
• Indexing (mini lecture)
• Alignment (mini lecture)
• Alignment, assembly, kmers (mini lecture)
• SAM, BAM, BED (mini lecture)
• Alignment QC (mini lecture)
• Abundance Estimation (mini lecture)
• HTSeq (mini lecture)
• Differential expression (mini lecture)
• Alignment free analysis with Kallisto (mini lecture)
• Alternative expression (mini lecture)

Advanced Sequencing Technologies & Bioinformatics Analysis (November 16-20, 2020. Virtual due to COVID-19)

Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site

Presentations:

• Next Generation Sequencing (Short Read) Technologies (lecture - Elaine Mardis)
• Long Read Sequencing (lecture - Dick McCombie)
• Single Cell Sequencing (lecture - Jon Preall)
• The application of epigenomic profiling strategies to study cancer and other common diseases (lecture - Peter Schacheri)

• Poisson processes in biology - Aaron Quinlan

• Intructor Introductions
• Introduction to Cloud Computing (lecture)
• Introduction to RNA Sequencing (lecture)

• Introduction to IGV (lecture)

• Fasta, Fastq, GTF (mini lecture)
• Indexing (mini lecture)
• Alignment (mini lecture)
• Alignment, assembly, kmers (mini lecture)
• SAM, BAM, BED (mini lecture)
• Alignment QC (mini lecture)
• Abundance Estimation and Differential Expression (lecture)
• Alignment free analysis with Kallisto (mini lecture)
• Alternative expression (mini lecture)
• Analysis and interpretation of single-cell RNA-seq data (lecture - Allegra Petti)

CBW Informatics for RNA-seq analysis (June 17-19, 2020. Planned for Montreal but VIRTUAL due to COVID-19)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

Presentations:

• Intructor Introductions
• Introduction to RNA Sequencing (lecture)

• Introduction to IGV (lecture)

• Fasta, Fastq, GTF (mini lecture)
• Indexing (mini lecture)
• Alignment (mini lecture)
• Alignment, assembly, kmers (mini lecture)
• SAM, BAM, BED (mini lecture)
• Alignment QC (mini lecture)
• Abundance Estimation (mini lecture)
• HTSeq (mini lecture)
• Differential expression (mini lecture)
• Alignment free analysis with Kallisto (mini lecture)
• Alternative expression (mini lecture)
• scRNA pt. 1 (lecture)
• scRNA pt. 2 (lecture)

CSHL Advanced Sequencing Technologies and Applications (November 5-17, 2019. Cold Spring Harbor, NY, USA)

Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site

Presentations:

• Introduction to Cloud Computing (lecture)
• Introduction to RNA Sequencing (lecture)

• Introduction to IGV (lecture)

• Fasta, Fastq, GTF (mini lecture)
• Indexing (mini lecture)
• Alignment (mini lecture)
• Alignment, assembly, kmers (mini lecture)
• SAM, BAM, BED (mini lecture)
• Alignment QC (mini lecture)
• Abundance Estimation (mini lecture)
• HTSeq (mini lecture)
• Differential expression (mini lecture)
• Alignment free analysis with Kallisto (mini lecture)
• Alternative expression (mini lecture)

CBW Informatics for RNA-seq analysis (June 11-13, 2019. Toronto, ON, Canada)

Organized by Canadian Bioinformatics Workshops (CBW) - Course Site

Presentations:

• Introduction to Cloud Computing (lecture)

• Introduction to RNA Sequencing (lecture)

• Fasta, Fastq, GTF (mini lecture)
• Indexing (mini lecture)
• Alignment (mini lecture)
• Alignment, assembly, kmers (mini lecture)
• SAM, BAM, BED (mini lecture)
• Alignment QC (mini lecture)
• Abundance Estimation (mini lecture)
• HTSeq (mini lecture)
• Differential expression (mini lecture)
• Alignment free analysis with Kallisto (mini lecture)
• Alternative expression (mini lecture)
• scRNA-seq (mini lecture)

CBW-CSHL High-Throughput Biology: From Sequence to Networks (March 11-17, 2019. Cold Spring Harbor, NY, USA)

Organized by Cold Spring Harbor Laboratory (CSHL) and Canadian Bioinformatics Workshops (CBW) - Course Site

Presentations:

• Module 7 - Introduction to RNA Sequencing (lecture)
• Module 8 - RNA-Seq Alignment and Visualization (lecture)
• Module 9 - Expression and Differential Expression (lecture)
• Module 10 - Reference Free Alignment (lecture)

• Module 11 - Isoform Discovery and Alternative Expression (lecture)

• Fasta, Fastq, GTF (mini lecture)
• Indexing (mini lecture)
• Alignment (mini lecture)
• Alignment, assembly, kmers (mini lecture)
• SAM, BAM, BED (mini lecture)
• Alignment QC (mini lecture)
• Abundance Estimation (mini lecture)
• HTSeq (mini lecture)
• Differential expression (mini lecture)
• Alignment free analysis with Kallisto (mini lecture)
• Alternative expression (mini lecture)

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)
• Introduction to IGV Browser (tutorial)
• Genome Analysis Platforms (lecture)

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)
• 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)
• 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)

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)
• 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)

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)
• Introduction to Genome Analysis Platforms (lecture)
• 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)

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)
• 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

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

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