Align two single cell experiments

Question

[elb]

Hi guys,

I'm trying to align two single cell experiments using the Seurat package. According to the tutorial here: https://satijalab.org/seurat/Seurat_AlignmentTutorial.html the standard pipeline first performs the FindVariableGenes step and then creates an object from the union of the two datasets. I would like to perform the regression on mt-genes and on cell cycle genes. My question is: when to perform the regression? On the single objects independently before the union or on the object from the union?

Thank you in advance!