RNA-seq Analysis 2023

Welcome

Welcome to Informatics for RNA-seq Analysis 2023.

The course schedule can be found here

Meet your faculty 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

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Class Photo

RNA-seq Analysis Class of 2023
RNA23 Workshop Social

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Day 1

Welcome

Nia Hughes

Module 0 Lecture Slides: Cloud Computing
Module 0 Lecture Slides: Introductions

Module 1

Module 1 Lecture Slides
Module 1 Mini-Lecture: FASTA/FASTQ/GTF
Module 1 Mini-Lecture: Indexing

Module 1 Lab

Introduction to Inputs
Reference Genomes
Annotations
Indexing
Data
Data QC

Module 2

Module 2 Lecture Slides
Module 2 Mini-Lecture: Alignment
Module 2 Mini-Lecture: Alignment vs. Assembly vs. Pseudoalignment
Module 2 Mini-Lecture: SAM/BAM/BED file formats
Module 2 Mini-Lecture: Alignment QC

Module 2 Lab

Introduction to Alignment
Adapter Trim
Alignment
IGV
Alignment Visualization
Alignment QC

Optional Team Assignment

Team Assignment - Alignment

• We will be completing the download and data preprocessing steps today

Day 2

Module 3

Module 3 Lecture Slides
Module 3 Mini-Lecture: Abundance Estimation
Module 3 Mini-Lecture: HTSeq
Module 3 Mini-Lecture: Differential Expression

Module 3 Lab

Introduction to Expression Analysis
Expression
Differential Expression
Ballgown DE Visualization
Batch Correction
DE Pathway Analysis

Day 3

Module 4

Module 4 Mini-Lecture: Alignment-Free Expression Estimation (Kallisto)

Module 4 Lab

Introduction to Alignment-Free Analysis
Alignment-Free Expression Estimation (Kallisto)