how does bdgcmp work?

[Moshe Olshansky]

Dear Tao,

Thank you very much for posting "Advanced: Call peaks using MACS2 subcommands". I discovered it only a few days ago and found it very informative.

I still have a question about what bdgcmp does. Is it correct that for every base it takes a 200 bp window centered at this base, summarizes all the pileups in the treatment and all the pileups in control in this window and then applies the requested statistic (for qpois it first applies ppois and then BH adjustment)? Or does it bin the genome into 200 bp bins and does the above to every bin? Or anything else?

Thank you,

Moshe.