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
Day 1
Welcome
Nia Hughes
Module 1
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
Complete Part I - Obtaining the dataset & reference files and Part II - Data Preprocessing.
Day 2
Module 3
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
Post-Workshop Materials
AMI
We have made our AWS AMI (Amazon Machine Image) publicly available. To launch your own instance, follow the instructions provided by Amazon on how to launch an EC2 instance from a custom Amazon Machine Image. Please note that you will need an AWS account to proceed, and that you will need to upload the CourseData files yourself.
Here are the details of the AMI:
- AWS Region: us-east-1 (N. Virgina)
- AMI type: public image
- AMI name: CBW_RNA_240613
- AMI ID: ami-0216fae97002bb976
If you want to create and activate a new AWS account, please follow the instructions provided by Amazon.