cooler version difference in parameters

[NMaziak]

Hello,

When running fanc to-cooler I got different results based on the cooler version as discussed here. I was wondering if the filtering could be changed to fit the previous version, since it does seem to be more aggressive after the new additions of mad_max, min_nnz, and min_count.

Thanks for all the help,
Noura

[kaukrise]

Hi Noura,

I have added the parameters you mentioned to to-cooler.

--mad-max MAD_MAX     Cooler balancing setting for bin filtering. Please see Cooler docs for details. Default is 5.
--min-nnz MIN_NNZ     Cooler balancing setting for bin filtering. Please see Cooler docs for details. Default is 10.
--min-count MIN_COUNT
                        Cooler balancing setting for bin filtering. Please see Cooler docs for details. Default is 0.

Could you please test it? You'll need to change the defaults to what they were before the version upgrade.

fanc-0.9.29b1.tar.gz

Best,
Kai

[NMaziak]

Hi Kai,

Amazing, will test it out over the weekend and let you know! I was wondering if the parameter for increasing the amount of iterations could also be included?

Best,
Noura