i try to peak calling for benchmark data by MACS2.
suppose i want to use subsection of genome chr1:3,000,000-3,100,000.
so this is my input : < JUN_K562.bam , JUN_control.bam >.
and i want to check result by to modify threshold value. like a Q value , broad-cutoff in broad calling.
however, if i slice JUN_control.bam by that region ( 3M to 3M + 100K ) same as JUN_K562.bam,
there is no change on result file even i keep modify Q-value. i don`t know why.
but when i try this with whole genome size control file, it was worked.
so, this is my question. when i want to peak calling with small subsection of genome,
control file must be whole genome size?