RNA-seq Analysis 2024

Welcome

Welcome to RNA-seq Analysis 2024.

The course schedule can be found here

Pre-Workshop Preparation

Pre-work including programs to install can be found here

AWS Module

Connecting and properly using a cloud computing cluster at the CBW here


Class Photo

RNA-seq Analysis Class of 2024


Course Materials

Coming soon!

Day 1

Welcome

Nia Hughes

Module 1

Module 1 Lecture Recording

Module 1 Lecture Slides - Intro
Module 1 Lecture Slides - FASTA/FASTQ/GTF
Module 1 Lecture Slides - Indexing

Module 1 Lab

Introduction to Inputs
Reference Genomes
Annotations
Indexing
Data
Data QC

Module 2

Module 2.1 Lecture Recording
Module 2.2 Lecture Recording

Module 2 Lecture Slides - Alignment
Module 2 Lecture Slides - Alignment vs Assembly vs Kmer
Module 2 Lecture Slides - SAM/BAM/BED
Module 2 Lecture Slides - IGV
Module 2 Lecture Slides - Alignment QC

Module 2 Lab

Introduction to Alignment
Adapter Trim
Alignment
IGV
Alignment Visualization Preparation
Alignment Visualization IGV
Alignment Visualization Allele Expression
Alignment QC

Optional Team Assignment

Team Assignment - Alignment

Complete Part I - Obtaining the dataset & reference files and Part II - Data Preprocessing.

Day 2

Module 3

Module 3 Lecture Recording

Module 3 Lecture Slides

Module 3 Lab

Introduction to Expression Analysis
Expression Analysis with Stringtie and htseq-count

Optional Team Assignment

Team Assignment - Alignment (Continued)

Complete Part III - Alignment and Part IV - Post-alignment QC & IGV Visualization.

Team Assignment - Expression and DE

Complete Part I - Expression Estimation.

Day 3

Module 3 Lab (Continued)

Differential Expression with Ballgown
Differential Expression with DESeq2
DE Visualization with Ballgown
DE Visualization with DESeq2
DE Visualization Advanced
DE Pathway Analysis
Batch Correction - Preparation
Batch Correction Analysis