Accurate expression quantification from nanopore direct RNA sequencing with NanoCount

Abstract

Sequencing full-length native RNAs using long-read direct RNA sequencing (DRS) has the potential to overcome many limitations of other sequencing methods that require RNA fragmentation, cDNA synthesis, or PCR. We developed NanoCount for fast, accurate transcript isoform quantification in DRS and demonstrate it outperforms similar methods. Using synthetic controls and human SH-SY5Y cell differentiation into neuron-like cells, we show that DRS accurately quantifies RNA expression and identifies differential expression of genes and isoforms. Our results demonstrate enhanced DRS isoform quantification with NanoCount and establish the ability of DRS to identify biologically relevant differential expression of genes and isoforms.