Accurate long-read transcript discovery and quantification at single-cell, pseudo-bulk and bulk resolution with Isosceles.

ABSTRACT: Accurate detection and quantification of mRNA isoforms from nanopore long-read sequencing remains challenged by technical noise, particularly in single cells. To address this, we introduce Isosceles, a computational toolkit that outperforms other methods in isoform detection sensitivity and quantification accuracy across single-cell, pseudo-bulk and bulk resolution levels, as demonstrated using synthetic and biologically-derived datasets. Here we show Isosceles improves the fidelity of single-cell transcriptome quantification at the isoform-level, and enables flexible downstream analysis. As a case study, we apply Isosceles, uncovering coordinated splicing within and between neuronal differentiation lineages. Isosceles is suitable to be applied in diverse biological systems, facilitating s

SUBMITTER: Kabza M 

PROVIDER: S-EPMC11345431 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature