None in maps

[yardenmatok203]

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]

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]

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]

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

I'm not familiar with allValidPairs format.

[yardenmatok203]

Do you know which library can I use? In my HIC data I have data with bins: 500, 1000, 1500,.... Thank you, Yarden

…

On Mon, Aug 14, 2023 at 12:48 AM David Kelley ***@***.***> wrote: Yes, for HiC NaNs regularly occur, and we interpolate to set the values. I'm not familiar with allValidPairs format. — Reply to this email directly, view it on GitHub <#171 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJYZ7Z2MMITZZ6YJYZTLDLLXVFDUVANCNFSM6AAAAAA24UZLXY> . You are receiving this because you authored the thread.Message ID: ***@***.***>