Workshop Schedule
Day 1
| Time | Topic | Instructor |
|---|---|---|
| 9:00 - 9:40 | Workshop Introduction | Radhika |
| 9:40 - 10:30 | Introduction to the Shell | Radhika |
| 10:30 - 10:45 | Break | |
| 10:45 - 11:35 | Introduction to the Shell (cont.) | Meeta |
| 11:35 - 12:15 | Searching and Redirection | Mary |
| 12:15 - 13:15 | Lunch | |
| 13:15 - 13:45 | Introduction to the Vim Text Editor | Radhika |
| 13:45 - 15:00 | Loops and Shell Scripts | Meeta |
| 15:00 - 15:15 | Break | |
| 15:15 - 15:45 | Permissions and Environment Variables | Mary |
| 15:45 - 17:00 | Introduction to High-Performance Computing for HMS-RC's O2 | Radhika |
Day 2
| Time | Topic | Instructor |
|---|---|---|
| 9:00 - 10:00 | Introduction to ChIP-seq | Meeta |
| 10:00 - 10:15 | Break | |
| 10:15 - 11:00 | Project Organization and Best Practices in Data Management | Radhika |
| 11:00 - 11:50 | Sequencing data QC using FastQC | Mary |
| 11:50 - 12:15 5 | Alignment theory | Meeta |
| 12:15 - 13:15 | Lunch | |
| 13:15 - 14:00 | Alignment and filtering of reads | Mary |
| 14:00 - 15:20 | Automating generation of alignment files | Radhika |
| 15:20 - 15:35 | Break | |
| 15:35 - 15:5 | ChIP-seq File Formats | Radhika |
| 15:55 - 17:00 | Peak calling with MACS2 | Meeta |
Day 3
| Time | Topic | Instructor |
|---|---|---|
| 9:00 - 9:20 | Peak calling with MACS2 (contd.) | Meeta |
| 9:20 - 10:20 | Assessing ChIP quality using cross correlation | Mary |
| 10:20 - 10:35 | Break | |
| 10:35 - 11:35 | Assessing Peak calls and ChIP quality using ChIPQC | Meeta |
| 11:35 - 12:00 | Handling Replicates with Bedtools | Radhika |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 13:50 | Handling Replicates with IDR | Radhika |
| 13:50 - 15:10 | Visualization and exploration of ChIP-seq data | Meeta |
| 15:10 - 15:25 | Break | |
| 15:25 - 15:50 | Qualitative assessment using IGV | Meeta |
| 15:50 - 16:20 | Functional analysis | Mary |
| 16:20 - 16:40 | Overview of ChIP-seq workflow | Meeta |
| 16:30 - 17:00 | Wrap-up and Survey | Radhika |