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

## TL;DR

GeneExt improves gene expression analysis in non-model species by refining gene annotations using single-cell RNA-seq data.

## Contribution

GeneExt is a novel tool that extends gene annotations using scRNA-seq data to enhance quantification in non-model species.

## Key findings

- Incomplete gene models in non-model species lead to poor gene expression quantification in scRNA-seq.
- GeneExt improves gene annotation accuracy and enhances biological interpretation of cell type atlases.
- The tool was tested on eight non-model organism datasets, showing its effectiveness.

## Abstract

Incomplete gene models negatively impact single-cell gene expression quantification. This is particularly true in non-model species where often gene 3ʹ ends are inaccurately annotated, while most scRNA-seq methods only capture the 3ʹ transcript region. This results in many genes being incorrectly quantified or not detected.

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.

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.