| layout | permalink | title | header1 | header2 | image | keywords | description | instructors | length |
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workshop_main_3day |
/Julia_Repo |
RNA-seq Analysis |
Workshop Pages for Students |
RNA-seq Analysis 2024 |
/site_images/CBW_RNA_seq_icon.jpg |
RNA-seq data, differential expression analysis, assemble transcripts |
Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. |
Malachi Griffith, Obi Griffith |
3 days |
Welcome to RNA-seq Analysis 2024.
The course schedule can be found here
Pre-work including programs to install can be found here.NOTE hello
Connecting and properly using a cloud computing cluster at the CBW here
RNA-seq Analysis Class of 2024
Nia Hughes
Module 1 Lecture Slides - Intro
Module 1 Lecture Slides - FASTA/FASTQ/GTF
Module 1 Lecture Slides - Indexing
Introduction to Inputs
Reference Genomes
Annotations
Indexing
Data
Data QC
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
Introduction to Alignment
Adapter Trim
Alignment
IGV
Alignment Visualization Preparation
Alignment Visualization IGV
Alignment Visualization Allele Expression
Alignment QC
Complete Part I - Obtaining the dataset & reference files and Part II - Data Preprocessing.
Introduction to Expression Analysis
Expression Analysis with Stringtie and htseq-count
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.
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
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.