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

Michal Kabza, Alexander Ritter, Ashley Byrne, Kostianna Sereti, Daniel Le, William Stephenson and Timothy Sterne-Weiler ()
Additional contact information
Michal Kabza: F. Hoffmann-La Roche Ltd
Alexander Ritter: Genentech Inc.
Ashley Byrne: Genentech Inc.
Kostianna Sereti: Genentech Inc.
Daniel Le: Genentech Inc.
William Stephenson: Genentech Inc.
Timothy Sterne-Weiler: Genentech Inc.

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: 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 studies of cellular heterogeneity across biomedical research applications.

Date: 2024
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-024-51584-3 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51584-3

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-024-51584-3

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().