Calling peaks genome-wide

[rikrdo89]

HI,
is there a way to call peaks genome-wide instead of the chromosome by chromosome? I guess I could make multiple chrxx_chrxx.txt files, and then concatenate all the calls, but i was hoping there was a more streamlined way of doing this.

[XiaoTaoWang]

Hi,
Perhaps I didn't understand you very well ... but if you already have a .cool file created, by default the pyHICCUPS distributed with this package can detect loops of all chromosomes for you, you don't need to concatenate the calls manually.