Posts
My thoughts and ideas
RNA-seq Bioinformatics
Introduction to bioinformatics for RNA sequence analysis
Lectures
Recorded lectures
- 2023 CBW course lectures (YouTube)
- 2021 CSHL course lectures (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)
Advanced Sequencing Technologies & Bioinformatics Analysis (November 9-22, 2025)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Overview of Next-generation Short Read Sequencing Technologies, Emerging platforms, and Experimental Design (Elaine Mardis)
- Long read sequencing technology and research applications (Richard McCombie)
- Single cell sequencing approaches (Jonathan Preall)
- Digital spatial profiling lecture (Elizabeth Garfinkle)
- Overview of bioinformatics lecture (Chris Miller)
- Intro to Cloud Computing Lab (My Hoang)
- Intro to Unix/command line lab (Felicia Gomez)
- File Formats (SAM/BAM/BED) (Felicia Gomez)
- Even more command line (Chris Miller) - Exercise
- DNA Alignment concepts (Felicia Gomez)
- IGV lab (Kartik Singhal)
- DNA Alignment Lab (Mariam Khanfar) - Exercise
- Intro to Variant Calling (Chris Miller)
- Ethics and Regulation of Genomic Research (Jessica Mozersky)
- Germline Variant Calling Lab (Chris Miller)
- Somatic Variant Calling (Chris Miller)
- Genomic intervals/Bedtools (Felicia Gomez)
- Bedtools lab (Jennie Yao, Mariam Khanfar) - Sandbox link
- Variant Representation and Annotation (Alex Wagner)
- VEP/Variant Annotation lab (Chris Miller)
- Intro to Docker and containers (Chris Miller) - Exercise
- CNV/SV detection (Chris Miller)
- CNV/SV lab (Charlz Jerold)
- Epigeneomics Lecture (Chris Miller)
- Epigenomics Lab - ChIPseq (Kartik Singhal)
- Diagnosing sequencing issues - What can go wrong, will (Chris Miller)
- Intro to R, data structures, and data manipulation (Katie Campbell)
- Data manipulation and intro to data visualization in RStudio (Katie Campbell)
- Data Munging/Cleaning - “star wars” lab (Kartik Singhal, Charlz Jerold)
- Introduction to bulk RNA-sequencing (Obi Griffith)
- Environment and tool installation lab (Obi Griffith)
- Reference genomes, transcript annotations, and indexing lab (Obi Griffith)
- RNAseq data and read QC lab (Obi Griffith)
- Alignment and visualization concepts lecture (Obi Griffith)
- Alignment lab (Obi Griffith)
- Alignment visualization lab (Malachi Griffith)
- Allele expression and visualization lab (Malachi Griffith)
- Post alignment QC lab (Malachi Griffith)
- Expression and Differential Expression analysis lecture (Obi Griffith)
- Expression analysis lab (Obi Griffith)
- Differential expression lab (Malachi Griffith)
- Differential expression visualization and interpretation lab (My Hoang)
- Differential expression pathway analysis lab (Obi Griffith)
- Batch correction lab (Malachi Griffith)
- Alignment free analysis lab (Malachi Griffith)
- Epi2Me: Direct RNA Modification Analysis on ONT (Matt Attreed, Oxford Nanopore)
- Massively Parallel Assays (Justin Kinney)
- Python Intro and pre-req review (Jonathan Preall, Claire Regan)
- Seminar: “Running NGS pipelines with NextFlow-Core” (Lara Ianov)
- Rapid WGS pediatric diagnostics (Bimal Chaudhari)
- Intro to Single Cell Analysis (Jonathan Preall)
- Basic scRNA visualization in Loupe (Jonathan Preall)
- Pandas and Data Visualization (seaborn, matplotlib) (Claire Regan)
- scRNA/ScanPy lab (Jonathan Preall)
- Cell Typing Lab (Jonathan Preall)
- Loading Spatial Datasets (Jonathan Preall)
- Computational methods for long read sequencing (Michael Schatz)
CBW RNA-seq analysis (July 7-9th, 2025. Ottawa, ON, Canada and Edmonton, AB, 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)
Cancer Research Institute Bioinformatics Bootcamp (May 16-22, 2025)
Organized by Cancer Research Institute (CRI) - Course Site
Presentations:
- Introduction to DNA and RNA sequencing (Obi Griffith and Malachi Griffith)
- Introduction to scRNA sequencing technology (Obi Griffith)
- Introduction to scRNA sequencing analysis (Malachi Griffith)
Advanced Sequencing Technologies & Bioinformatics Analysis (November 10-23, 2024)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Emerging next-generation sequencing platforms (Elaine Mardis)
- Long read sequencing technology and research applications (Richard McCombie)
- Single cell sequencing technology and applications (Jonathan Preall)
- Spatial Transcriptomics (Corinne Strawser)
- Ethics and Regulation of Genomic Research (Jessica Mozersky-virtual lecture)
- An Overview of Bioinformatics (Felicia Gomez)
- Introduction to Unix/Command Line Lab (Felicia Gomez)
- Intro to cloud computing (My Hoang)
- More advanced command line lab and exercise (Jason Kunisaki)
- File formats (Mariam Khanfar)
- Alignment concepts (Felicia Gomez)
- Genomics in Agriculture (Zach Lippman)
- Concepts in genome coordinates, intervals, and arithmetic (Mariam Khanfar)
- Using bedtools to perform genome arithmetic (Jason Kunisaki)
- Bioinformatics in Python (Jason Williams)
- DNA Alignment LAB (Mariam Khanfar)
- Massively Parallel Assays (Justin Kinney)
- Introduction to R (Katie Campbell)
- Introduction to IGV (Kartik Singhal)
- Introduction to bulk RNA-sequencing (Malachi Griffith)
- Environment and tool installation lab (Obi Griffith)
- Reference, annotations, indexing, data and QC lab (Obi Griffith)
- Alignment lab (Arpad Danos)
- Alignment and visualization concepts(Arpad Danos)
- Alignment visualization lab (Malachi Griffith)
- Post alignment QC lab (Malachi Griffith)
- Introduction to Expression and Differential Expression Analysis (Obi Griffith)
- Expression and Differential Expression analysis (Obi Griffith)
- Expression analysis lab (Obi Griffith)
- Differential expression lab (My Hoang)
- Differential expression visualization and interpretation lab (Malachi Griffith)
- Differential expression pathway analysis lab (Obi Griffith)
- Batch correction lab (Malachi Griffith)
- Alignment free analysis lab (Malachi Griffith)
- Introduction to epigenomics - ATAC, ChIPseq and Bisulfite approaches (Chris Miller)
- Epigenomics lab - Peak Calling (Kartik Singhal)
- Long Read Sequencing (Chris Miller)
- Long Read Sequencing (RNAseq) Lab (My Hoang)
- Data Visualization with R (Chris Miller)
- Data Cleaning (Chris Miller)
- Intro to concepts in variant calling (Chris Miller)
- Germline Variant Calling Lab (Chris Miller)
- Somatic Variant Calling Lab (Mariam Khanfar)
- Copy Number and Structural Variants (Chris Miller)
- Copy Number and Structural Variants_Lab (Chris Miller)
- Bioinformatics with Python (Alex Wagner)
- Bioinformatics with Pythone_Lab
- Variant Representation and Annotation (Alex Wagner, Daniel Puthawala)
- Variant Representation and Annotation_Lab
- Rapid WGS Pediatric Diagnostics (Bimal Chaudhari)
- Introduction to scRNA analysis (Jonathan Preall)
- Single cell ATAC-seq (Yang Li)
- What’s New in the Human (pan)genome? (Adam Phillippy)
CBW RNA-seq analysis (June 17-19th, 2024. 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)
Cancer Research Institute Bioinformatics Bootcamp (April 27, 2024-May 2, 2024)
Organized by Cancer Research Institute (CRI) - Course Site
Presentations:
- Introduction to DNA and RNA sequencing (Obi Griffith and Malachi Griffith)
- Introduction to scRNA sequencing technology (Obi Griffith)
- Introduction to scRNA sequencing analysis (Malachi Griffith)
Advanced Sequencing Technologies & Bioinformatics Analysis (November 6-19, 2023)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Emerging next-generation sequencing platforms (Elaine Mardis)
- Overview of Next Generation Short Read Sequencing Technologies (Elaine Mardis)
- Epigenomics (Ben Sunkel)
- The Genomic Era is Alive and Well! (John McPherson)
- Research Applications of Single Cell Sequencing (Trevor Pugh)
- Single cell sequencing technology and applications (Jonathan Preall)
- Genomics at scale with the NHGRI AnVIL (Mike Schatz)
- Long read sequencing technology and research applications (Richard McCombie)
- Genomics in agriculture(Zach Lippman)
- Interpreting cis-regulatory mechanisms learned by genomic deep learning (Peter Koo)
- More advanced command line lab and exercise (Jason Kunisaki)
- What’s new in the human (pan)genome?(Adam Phillippy)
- An Overview of Bioinformatics (Chris Miller)
- Intro to cloud computing (My Hoang)
- [Spatial transcriptomics (Sanja Vickovic)]
- Concepts in genome coordinates, intervals, and arithmetic (Jason Kunisaki)
- Using bedtools (and awk) to perform genome arithmetic (Jason Kunisaki)
- Noncoding RNAs (Chris Maher)
- File formats (Felicia Gomez)
- Alignment concepts (Felicia Gomez)
- Ethics and Regulation of Genomic Research (Jessica Mozersky)
- DNA Alignment LAB_CSHL_2023 (Mariam Khanfar)
- Introduction to IGV (Kartik Singhal)
- Intro to concepts in variant calling (Chris Miller)
- VCF Format (Mariam Khanfar)
- Somatic variant calling (Chris Miller)
- Variant Representation and Interpretation (Wes Goar)
- Introduction to epigenomics - ATAC, ChIPseq and Bisulfite approaches (Chris Miller)
- Data Visualization(Chris Miller)
- Data Cleaning (Chris Miller)
- Single cell ATAC-seq (Yang Li)
- Single cell ATAC-seq Part 2 (Yang Li)
- Introduction to bulk RNA-sequencing (Malachi Griffith)
- Alignment and visualization concepts(Arpad Danos)
- Expression and Differential Expression analysis lecture (Obi Griffith)
- Probability and statistics for genomics analysis (Aaron Quinlan)
- Probability and statistics for genomics analysis Part 2 (Aaron Quinlan)
- Introduction to scRNA analysis (Jonathan Preall)
- Epilepsy-affected brain tissues, somatic mosaicism, model organisms (Tracy Bedrosian)
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)
- Intructor Introductions
- 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 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)
- 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)
- 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)
- 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