I currently use CellRanger on single nucleus RNA-seq data using the pre-mRNA reference that they advise. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references
I want to try using Kallisto Bustools for increased processing speed. However, I haven't seen it used yet with single nucleus data, where there are a high proportion of introns, which won't be presented in the standard cDNA reference that one uses to build an index.
Is there a reference transcriptome for human that has unspliced mRNA?
Or does anyone have any references for using Kallisto with nuclear RNA?