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