GeneExt takes as input scRNA-seq mapped reads and a gene annotation file (GTF or GFF, any version) and outputs an extended gene annotation file for improved scRNA-seq transcript quantification.

Installation

Note: Only Linux is recommended for this program given the availability of bioinformatics Python libraries.

Note: Users lacking a Conda installation are recommended to install Miniforge.

Tool dependencies can be installed with conda or mamba:

# create environment
export CFLAGS="-fno-finite-math-only" && conda env create -n geneext -f environment_updated.yaml

# activate environment
conda activate geneext

Test run

Once dependencies are installed, try running GeneExt with sample data:

python3 geneext.py -g test_data/annotation.gtf -b test_data/alignments.bam -o result.gtf --peak_perc 0

Note1: --peak_perc 0 is set to 0 to disable peak filtering as the test dataset is too small.
Note2: GeneExt has been mostly tested on gtf-formatted files. Please, use gtf, if possible.

Please, first test whether the tool works properly on the test data! Most errors with GeneExt come from improperly formatted files. If you encounter errors, please, try standardizing your annotation file with AGAT.

For details on how to obtain alignment file, please refer to the manual.
If problems persist, don't hesitate to contact the authors.

Citation

If you use this tool, please cite:

Zolotarov, G., Grau-Bové, X., & Sebé-Pedrós, A.
GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis
bioRxiv 2023.12.05.570120
https://doi.org/10.1101/2023.12.05.570120