| 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 |