Chipseq Data Paired End Macs2 Results Validation

Question

[ramzz.1987]

Hii Stars,

I am newbie in chipseq data analysis , so please help in validating the macs2 results what are the important factors to consider to judge good and bad results ,how to interpret the results , and what files can we use , please provide links of journals if any explaining about results of macs2 peak annotation steps

Answer 1

[arnstrm]

I would recommend IDR (for quality check and measuring replicates consistency). You can use either SPP or MACS for peak calling. You can find the explanation as well as step by step guide to perform analyses and choose the reliable peaks on that website. Also there is a attached documentation for understanding IDR (IDR 101). For annotation, CEAS is a good choice. You can also use PeakAnalyzer (finds nearest TSS), GREAT. Finally, you can use ngsplot to generate some plots.