| Time | Topic | Instructor |
|---|---|---|
| 9:00 - 9:15 | Introduction to Workshop | Radhika |
| 9:15 - 10:00 | Introduction to ChIP-seq | Dr. Shannan Ho Sui |
| 10:00 - 10:10 | ChIP-seq Analysis Overview | Meeta |
| 10:10 - 10:20 | Break | |
| 10:20 - 11:20 | Unix review and Working in an HPC environment | Radhika |
| 11:20 - 11:50 | Project Organization and Data Management | Meeta |
| 11:50 - 12:50 | Sequence Data QC using FastQC | Mary |
| 12:50 - 13:50 | Lunch | |
| 13:50 - 14:05 | Alignment theory | Meeta |
| 14:05 - 15:05 | Alignment and filtering of reads | Mary |
| 15:05 - 15:15 | Break | |
| 15:15 - 16:15 | Automating generation of alignment files | Radhika |
| 16:15 - 16:30 | ChIP-seq File Formats | Radhika |
| 16:30 - 17:00 | Peak calling with MACS2 | Meeta |
| Time | Topic | Instructor |
|---|---|---|
| 9:00 - 9:20 | Peak calling with MACS2 (cont'd) | Meeta |
| 9:20 - 10:40 | Assessing Peak calls and ChIP quality using ChIPQC | Mary |
| 10:40 - 10:50 | Break | |
| 10:50 - 11:25 | Handling Replicates | Radhika |
| 11:25 - 12:10 | Differentially enriched peaks using DiffBind | Meeta |
| 12:10 - 13:10 | Lunch | |
| 13:10 - 14:00 | Visualization and exploration of ChIP-seq data | Meeta |
| 14:00 - 14:45 | Qualitative assessment using IGV | Radhika |
| 14:45 - 14:55 | Break | |
| 14:55 - 16:15 | Functional analysis and Motif Analysis | Mary |
| 16:15 - 16:45 | Overview of ChIP-seq workflow | Meeta |
| 16:45 - 17:00 | Wrap-up and Survey | Radhika |