This workshop will teach the basic concepts and practical aspects of ChIP-Seq data analysis. Topics covered will include: experimental approach, quality control, peak calling, and basic biological interpretation. No computer is required for this class, there is no hands-on work.
9:30-10:30 “ChIP-seq considerations”
This section will focus on the importance of experimental design in ChIP-seq. Topics include: variations on ChIP-seq, inputs, replicates, the limitations of ChIP-seq, and the value of follow-up analyses.
10:30-12:00 “Analysis of ChIP-seq data”
This section will focus on the analytical pipeline that is implemented by CCBR and NCBR. Time will be spent discussing the tools used, why they were chosen, and how to make sense of their outputs. Example results will be shown. Topics include: quality control and read alignment, deduplication, normalization, gene coverage plotting, peak calling, motif analysis, and more.