[Question] Mad-max filter

[jeff-godwin]

Hello,

I have a question regarding the filtering of low count bins.

The nextflow (v2.1.0) results produces balanced cooler files. Am I correct to assume this is from the "cooler balance" functionality? And is the --mad-max parameter running on the default value of 5 (https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance) ?
In HiCexplorer, one can calculate the mad-max filter using (https://hicexplorer.readthedocs.io/en/latest/content/tools/hicCorrectMatrix.html). Over here, open2c/cooler#140, it is mentioned that both filtering are equivalent. I want to clarify if the balance cool file needs any further filtering?

Many thanks,
Jeffrey

[nservant]

Hi @jeff-godwin

Until now, we were not changing the default parameter from cooler balance. So the --mad-max option was set by default.
However, I just added a new option --balancing_optswhich allow you to tune the balancing options when running the pipeline.
The new option has been added to the devbranch, and should hopefully be released soon