Input data matrix from Seurat toolkit analysis for RNA velocity analysis using scvelo

Question

[sarahmanderni]

Hi,

I have done the scRNAseq analysis follwoing seurat toolkit vignette (SCTtransform + integrate + clustering) and now planning to run RNA velocity analysis using scvelo tool. Is it reasonable to use the SCT assay, data slot as data matrix (adata.X) for scvelo? Of course the unprocessed spliced and unspliced layers will also be added as the layers to the obj from loom files. I am thinking maybe the data matrix (adata.X) is not anyway deterministic to calculate the velocities as the ratio of spliced to un-spliced will be used for this purpose?