For some of our snRNA-seq samples we are finding low fraction of reads detected in single-nuclei rna-seq samples from cellranger, while the other metrics are perfect.
While I understand this could be caused by library preparation and abundance of ambient RNA. Just wondering if this behavior is expected for single-nuclei datasets. My confusion is specifically coming from the fact that 10X website also has such a sample that has low number of fraction reads in cells.
Would love to know if this behavior is expected or seen often who are more experienced in snRNA-seq. The metric documentation page is here