| Time | Topic : Details |
|---|---|
| 9:00 | Introductions and Startup |
| 9:20 | Sequence QC: |
| Warming Up | |
| Quality Control (FASTQs) | |
| Trimming and MultiQC | |
| 11:00 | Break |
| 11:15 | Alignment: |
| Reference genomes | |
| Alignment | |
| 1:00 | Day 1 concludes |
| 9:00 | Review |
| 9:10 | Quantification: |
| Count matrix / Alignment QC | |
| Additional details and exercise | |
| 11:00 | Break |
| 11:15 | Groups and Modeling: |
| Intro to DESeq2 | |
| DESeq2 Initialization | |
| Count normalization and model fitting | |
| 1:00 | Day 2 concludes |
| 9:00 | Review |
| 9:10 | Expression plots: |
| Sample visualizations for QC | |
| 11:00 | Break |
| 11:15 | Differential Expression: |
| Comparisons | |
| DE Visiualization and Annotation | |
| Bonus Content | |
| 12:45 | Wrap-up |
| 1:00 | Day 3 concludes |