I first mapped to mm10 with bowtie and them did peak calling with macs using genome size 1800000000. Returned 6,632 regions with 3100+ for those high score peaks.
Then I wanted to use the histone modification etc. data from encode but those are in mm9 so I repeat everything using mm9 with all the other parameters the same except the genome size 1865500000 (which I assume it's not much difference) And I chose 'Perform the new peak detection method (futurefdr)' for mm9. However only 3,535 regions returned with high scores at ~1500.
I am confident for the mm10 analysis. But can't understand why mm9 result differs so much.
Thanks to anybody who can help me with that.