Workshop Schedule

Day 1

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

Day 2

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