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      RNA-Seq Analysis

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
RNA Sequencing Technologies - Dr. Lutz Froenicke
Support
Zoom
Slack
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI
R
Cluster Computing
Data Reduction
Files and Filetypes
Prepare dataset
Preprocessing raw data
Indexing a Genome
Alignment with Star
Generating counts tables
Alignment/Counts with Salmon (Extra)
Data analysis
Prepare R for data analysis
Annotation from BioMart
Differential Expression Analysis
DE Quizzes R Code
Pathway Analysis
Enrichment Quizzes R Code
Comparison between STAR and Salmon
ETC
Closing thoughts
Workshop Photos
Github page
Report Errors
Biocore website

Command Line Interface

A basic understanding of the command line interface (CLI) is highly recommended for success in this course. We will briefly review the commands necessary for this course on the first morning, but there will not be enough time to provide full instruction in CLI basics. Beginners without any previous knowledge will be able to complete this course, and achieve a more thorough understanding of the techniques and analyses covered, but will probably not be able to conduct an experiment on their own.

If you do not have CLI experience, or it has been a while since you last worked on the command line, please take some time before the workshop to work through the first part of the Introduction to the Command Line for Bioinformatics course.

Of course, you are free to continue working through all the materials in Introduction to the Command Line for Bioinformatics! The more confident you are in your command line skills, the more you will be able to explore the content in this course.