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

Abstract

AbstractIncomplete gene models can negatively impact single-cell gene expression quantification. This is particularly true in non-model species where often 3’ ends are inaccurately annotated, while most single-cell transcriptomics methods only capturing the 3’ transcript region. As a result, many genes are incorrectly quantified or not detected at all. Here, we introduce a tool that leverages 3’-end single-cell transcriptomics data to refine gene annotations. We exemplify its usage and its impact on the gene expression quantification of seven 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.