Are default copykat settings appropriate for single nucleus RNAseq?

navinlabcode / copykat

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Are default copykat settings appropriate for single nucleus RNAseq? #59

Closed TatyanaLev closed 2 years ago

TatyanaLev commented 2 years ago

Hi,

I am interested in using copykat to infer CNV in the RNA portion of multiome, which is single nucleus data. Do you strongly recommend changing anything from the examples in the tutorial?

Thanks!

gaobio commented 2 years ago

It should work. Try to use different LOW.DR to retain more genes in the analysis.