Viral load analysis in host organism cells

[tkapello]

Hi all,

I was wondering whether there is a consensus about how to test viral infection of cell types in a scRNA-seq dataset. I have mapped my reads to viral genomes and I have a matrix of viral genes x cell barcodes. I want to investigate which clusters are infected but I am not sure whether to use the nCount_RNA or nFeature_RNA. Is there a standard pipeline in the field?

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful. As this is not a question about the Seurat package itself I'm going to move this to discussion section and hopefully other members of community working on similar projects can chime in.

Best,
Sam