Using InferCNV for PBMCs

[Urja25]

Hi,

I am trying to use snRNAseq data from multiome PBMC datasets to run inferCNV.
I am using snRNAseq data from 10X Genomics PBMC dataset as normal reference for each "patient" PBMC dataset.
I am noticing very similar copy number changes across all patient samples.
I then also tried using a scRNAseq healthy PBMC dataset as reference but I am still noticing very similar CNV patterns in the patients, and this is something we don't expect.

What could I do to infer CNVs from PBMCs correctly?

Thanks a lot!