How to create custom snap.genome?

[priscilla-glenn]

Hi,
I need to use a masked mm39 genome and was searching the snapATAC2 website to try to figure out how I can add my own custom reference. I found "snapatac2.genome.Genome" but it doesn't have more details on what it does exactly. Is there another function that I have missed? In the future, I'll also want to analyze horse and cow, so if there is a way to create and add a custom snap.genome, that would be awesome.

Thanks!
Priscilla

[kaizhang]

The genome object is not strictly necessary. Each function in SnapATAC2 can take custom gff files or fasta file as input instead of the Genome object. See this for example: https://kzhang.org/SnapATAC2/reference/_autosummary/snapatac2.pp.import_data.html#snapatac2.pp.import_data

[priscilla-glenn]

Thank you!