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

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 quantifi...

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Bibliographic Details
Published in:Nature communications 2024-08, Vol.15 (1), p.7316-12
Main Authors: Kabza, Michal, Ritter, Alexander, Byrne, Ashley, Sereti, Kostianna, Le, Daniel, Stephenson, William, Sterne-Weiler, Timothy
Format: Article
Language:English
Subjects:
631/114
631/114/2397
631/1647/514/1949
631/208/212/2019
631/337/2019
Accuracy
Animals
Cell differentiation
Coffee
Computational Biology - methods
Gene Expression Profiling - methods
Gene sequencing
Heterogeneity
Humanities and Social Sciences
Humans
Isoforms
Medical research
Methods
Mice
multidisciplinary
Nanopore Sequencing - methods
Neurons - metabolism
Protein Isoforms - genetics
Protein Isoforms - metabolism
RNA, Messenger - genetics
RNA, Messenger - metabolism
Science
Science (multidisciplinary)
Sequence Analysis, RNA - methods
Single-Cell Analysis - methods
Software
Toolkits
Transcriptome - genetics
Transcriptomes
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Description
Summary: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. Analysis of nanopore long-read sequencing is challenged by technical noise, particularly in single cells. Here, authors introduce Isosceles, a toolkit for accurate isoform detection, quantification, and flexible downstream analysis of long-read data at single-cell, pseudo-bulk and bulk resolutions.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-024-51584-3