Accurate quantification of single-nucleus and single-cell RNA-seq transcripts

The presence of both nascent and mature mRNA molecules in single-cell RNA-seq data leads to ambiguity in the notion of a “count matrix”. Underlying this ambiguity, is the challenging problem of separately quantifying nascent and mature mRNAs. We address this problem by relating k-mer assignment to read assignment in the context of different classes of molecules, and describe a unified approach to quantifying both single-cell and single-nucleus RNA-seq.