RNA-seq Demystified

Setup instructions

Shared Google Doc

Schedule

Time	Topic	Instructor
Day 1
9:00	Workshop Introduction	Chris Gates
9:15	Warming Up	Travis Saari
	Quality Control
	Optional - Trimming and MultiQC
10:30	Break
	Reference Genomes
	Sequence Alignment and Gene Quantification with STAR/RSEM
	MultiQC and Count Matrix
	Optional - Additional Information
1:00	Day 1 concludes
Day 2
9:00	Intro Day 2	Chris Gates
9:10	Introduction to DESeq2	Dana King
	DESeq2 Initialization
10:15	Break
	Count Normalizations and DESeq2 model fitting
	Sample Visualizations for Quality Control
11:15	Break
	DE Comparisons and Gene Annotations
	DE Visualizations and output files
	Bonus - sample level QC visualizations
12:45	Wrap-up	Chris Gates