I have the ChIP seq of H3K27me3 in my sample. I in analyzing in Galaxy. When I compare my bigwig files and bed files (after MACS peak calling), I see that there are many peaks which are appearing when I visualize the bigwig files but not in bed files. I guess it should be something to do with MACS peak calling function parameters. When I set both the FDR to 0.4 and the broad peaks cut off to 0.4, then the peaks appear but I guess these values are too high. Which other parameters I can play with in MACS to get all the peaks.