add viral genes/reporter gene to existing analysis

[gianfilippo]

Hi,

I have data with some samples infected by a virus.
A first analysis has already been done without considering viral genes, as initially this was not a question.
Now we may want to identify the infected cells.
After remapping the samples including the viral genome and gene definition, is it possible to add the viral genes to the existing Seurat objects, without having to rerun the entire analysis ?
CellRanger output files are almost identical, but now include the extra genes and a few more cells, which we could probably disregard at this point.
The main purpose is to identify infected cells within the existing analysis, so, for now, use the viral genes just like a reporter gene.
In this context I would renormalize only for plotting purpose. Correct ?
Otherwise, would it make sense to rerun from scratch ? in this case the viral genes may be included as variable genes and drive some of the clustering. Or exclude them from the variable gene list ?

Thanks