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

Tool dependencies can be installed with conda or mamba:

# create environment
conda env create -n geneext -f environment.yaml

# activate environment
conda activate geneext

Test run

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

python 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!

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