Clarification on inclusion of intronic reads in filtered_feature_bc_matrix.h5 for snRNA-seq with Cell Ranger ARC

[Erfan1369]

Hello Seurat developers!

I am analyzing snRNA-seq data generated with 10x Multiome and processed through Cell Ranger ARC v2.0.2. The filtered_feature_bc_matrix.h5 was created using using a custom reference built from Ensembl GTF (GRCm39, Gencode vM33).

My questions are:

In Seurat, should snRNA-seq datasets processed with exonic-only counts still be normalized and analyzed in the same way as pre-mRNA (exon+intron) datasets?

Does Seurat provide any functionality (or recommended pipeline) to incorporate intronic reads separately (e.g., via velocyto spliced/unspliced matrices), or is this always handled externally?

The goal is to ensure that my downstream clustering, DE, and integration are being interpreted correctly given that the .h5 is likely exonic-only.

Thanks