calico/basenji

None in maps

Opened this issue · 4 comments

yardenmatok203 commented

Hey,

Is it possible to have nan in input\prediction?

Also, there are regions in the genome that are problematic, did you ignore them?

Thanks,
Yarden

davek44 commented

NaNs indicate that something has gone wrong. Yes, the training data creation stage uses a blacklist of regions that frequently encounter problematic read mapping.

yardenmatok203 commented

where can I find this blacklist?

also, I see there is a variable "seq_hic_nan", so can it be that some of the values are nan?

last question, I have "allValidPairs" format, how can I create cool in your binsize\format?

Thanks,
Yarden

davek44 commented

Yes, for HiC NaNs regularly occur, and we interpolate to set the values.

I'm not familiar with allValidPairs format.

yardenmatok203 commented