What are the differences in how the raw data is handled? What should we expect in how the data may look different at the QC metric stage from whole cell single cell RNA-Seq? Do any adjustments need to be made for analysis pipelines?
One thing to consider in the analysis step would be using a reference that has both Intronic and exonic regions as single-nuclei RNA-seq assay captures unspliced pre-mRNA as well as mature mRNA. A custom pre-mRNA reference package can be easily created from an existing Cell Ranger reference.
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