Hello, I have question related to Faire-seq peak calling. Since I am not a Linux user, I have only access to MACS2 (on galaxy) and PeakDEck. I have 4 faire-seq libraries generated from MEFS (WT and KO) in duplicate each. After quality check, filtering and mapping I merged the duplicates to use for peak calling. I ended up with 40000 to 90000 peaks per genotype using respectively MACS2 and PeakDEck. I used bed tools (bed intersect) to find the peaks that are present in both genotypes and I ended with 22000 peaks. Then of course extract reads from the bam files and feed them to EdgeR or DEseq.
I have seen that some people use the same strategy to analyze this kind of Data. However, I still think that we missing lots of information because the analysis is focused only on the peaks that are present in both genotypes. What about the one that are unique to each genotype?? Is there any other way of analyzing these data???