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GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis.

Grygoriy Zolotarov·Xavier Grau-Bové·Arnau Sebé-Pedrós
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Abstract

MOTIVATION: Incomplete gene models negatively impact single-cell gene expression quantification. This is particularly true in non-model species where often gene 3' ends are inaccurately annotated, while most scRNA-seq methods only capture the 3' transcript region. This results in many genes being incorrectly quantified or not detected. RESULTS: GeneExt leverages scRNA-seq data to refine gene annotations. We exemplify GeneExt usage and its impact on the gene expression quantification of eight non-model organism single-cell atlases. By extending and homogenizing gene annotations, our tool will help improve biological interpretation and cross-species comparisons of cell type expression atlases. AVAILABILITY: GeneExt is available at https://github.com/sebepedroslab/GeneExt (DOI: https://doi.org/10.5281/zenodo.18712940) under a GNU General Public license, together with test data and usage instructions.

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SoftwareSingle-Cell Gene Expression AnalysisRNA-SeqAnimalsSingle-Cell AnalysisModels, GeneticSequence Analysis, RNAHumansMolecular Sequence AnnotationJournal ArticleResearch Support, Non-U.S. Gov't

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Grygoriy Zolotarov, Xavier Grau-Bové, Arnau Sebé-Pedrós. 2026-02-28. GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis.. https://doi.org/10.1093/bioinformatics%2Fbtag094

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