Workshop Schedule
Day 1
| Time | Topic | Instructor |
|---|---|---|
| 9:00 - 9:40 | Workshop Introduction (slides) | Radhika |
| 9:40 - 10:40 | Introduction to the Shell | Radhika |
| 10:40 - 10:55 | Break | |
| 10:55 - 11:25 | Introduction to the Shell (contd.) | Meeta |
| 11:25 - 12:00 | Searching and Redirection | Mary |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 13:20 | Introduction to the Vim Text Editor | Mary |
| 13:20 - 14:35 | Loops and Shell Scripts | Meeta |
| 14:35 - 15:05 | Permissions and Environment Variables | Radhika |
| 15:05 - 15:20 | Break | |
| 15:20 - 16:00 | Project Organization and Best Practices in Data Management | Meeta |
| 16:00 - 17:00 | Introduction to RNA-seq workflow (slides) | Radhika |
Day 2
| Time | Topic | Instructor |
|---|---|---|
| 9:00 - 9:45 | Introduction to High-Performance Computing (slides) | Radhika |
| 9:45 - 10:30 | RNA-seq analysis workflow - Quality Assessment | Meeta |
| 10:30 - 10:45 | Break | |
| 10:45 - 11:15 | RNA-seq analysis workflow - Quality Assessment | Meeta |
| 11:15 - 11:45 | Genome builds and alignment strategies (slides) | Meeta |
| 11:45 - 12:30 | RNA-seq analysis workflow - Alignment and Counting | Mary |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 14:20 | RNA-seq analysis workflow - Alignment and Counting (contd.) | Mary |
| 14:20 - 15:20 | Automating the RNA-seq workflow | Radhika |
| 15:20 - 15:35 | Break | |
| 15:35 - 15:45 | Alternative workflows for analyzing RNA-seq data (slides) | Radhika |
| 15:45 - 16:45 | Quantifying expression using alignment-free methods (Salmon) | Mary |
| 16:45 - 17:00 | Wrap-up, Discussion, Q&A (slides) | Radhika |
Contact Info:
Webpage: http://bioinformatics.sph.harvard.edu/
Email: hbctraining (at) hsph (dot) harvard (dot) edu
Twitter: https://twitter.com/bioinfocore
Training materials: https://hbctraining.github.io/main/