I have done ChIP-seq for a transcription factor in two biological duplicates. Peaks were called using GEM on both the replicates. the first replicate gave around 48, 000 peaks while the second replicate gave 1, 80, 000 peaks. FRIP for these replicate was 5% and 43% respectively. Interestingly, 93% of peaks in the first replicate were common with the second replicate. Right now, I am planning to take the intersection of the two peak set for further analysis. I am not sure if it will create a problem while publishing. Please suggest if I need to do more any more statistical analysis before going for further analysis.
P.S. MEME analysis of intersect peaks shows enrichment of 2 motifs. Thanks
Hii, Thanks for comments ! I have done the IDR analysis. 18,000 of our 45,000 common peaks could pass the IDR of 1%.
Is it OK. ?