Informatics for RNA-Seq Analysis 2020


Welcome to Informatics for RNA-Seq Analysis 2020.

The course schedule can be found here.

Meet your faculty here

Pre-Workshop Preparation

Laptop Setup Instructions

Instructions to setup your laptop can be found here.

Pre-workshop Tutorials

Pre-readings and pre-work can be found here here.

It is in your best interest to complete these before the workshop.

Class Photo

Class Photo

Day 1

For all days please refer to content on


Rachade Hmamouchi

Module 0: Introduction to Compute Canada & Setup

Pierre-Oliver/Obi Griffith

Compute Canada Introduction

Connecting to the CC Cluster Lab Practical

Module 1: Introduction to RNA Sequencing Analysis

Malachi Griffith and Obi Griffith

Intro to RNA-seq Lecture

FASTA_FASTQ_GTF mini lecture

Indexing mini lecture

Module 1 Lab


Reference Genomes




Data QC

Module 2: RNA-seq Alignment and Visualization

Obi Griffith and Malachi Griffith

Alignment mini lecture

Alignment vs Assembly vs kmer mini lecture

SAM BAM BED mini lecture

IGV Tutorial lecture

Alignment QC mini lecture

Module 2 Lab

Adapter Trim



Alignment Visualization

Alignment QC

Team Assignment

Kelsy Cotto and Huiming Xia

Team Assignment Questions

Day 2

Module 3: Expression and Differential Expression

Obi Griffith and Malachi Griffith

Abundance Estimation mini lecture

HTSeq mini lecture

Differential Expression mini lecture

Module 3 Lab


Differential Expression

DE Visualization

Module 4: Reference Free Alignment

Malachi Griffith

Alignment Free - Kallisto mini lecture

Module 4 Lab


Team Assignment

Kelsy Cotto and Huiming Xia

Team Assignment Questions

Day 3

Module 5: Single-cell RNA-seq

Allegra Petti

Lecture - Part 1

Lecture - Part 2

Module 5 Lab

Single-cell RNAseq using Seurat

additional resources


Could you please 2min of your time ? here ***