Q: about the 'max-gap 'parameter

[liuyu988]

HI, I need to call broad peaks for histone mark. then i used -broad -max-gap parameters. but i met some questions.

first:

macs2 callpeak -t A.sorted.bam -n A --nomodel -g hs -f BAMPE --outdir 250_0.001 --broad -p 0.001 --broad-cutoff 0.001 --max-gap 250

macs2 callpeak -t A.sorted.bam -n A --nomodel -g hs -f BAMPE --outdir 250_0.001 --broad -p 0.001 --broad-cutoff 0.001 --max-gap 750

the difference between this two conditions is just max-gap. In my opinion, the max-gap won't influence the cutoff of calling peaks. but i found the number of peaks in 750 will be more than in 250. i'm so confused. when i saw the enrichment of histone mark in iGV, i noticed the peaks called by max-gap 750 were not called by max-gap 250.

could anyone can help me ? thanks a lot!!
YU