| 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 |