ScanExitron

A computational workflow for exitron splicing identification from RNA-Seq data.

🌟 Features

• Accurate Identification: High-performance detection of exitrons (exonic introns) directly from aligned RNA-Seq reads (BAM/CRAM).
• VCF Conversion: Built-in support to convert results into standard VCF files for downstream variant analysis.
• Bioconda Support: Easy deployment along with all underlying command-line dependencies.

🚀 Installation

Option 1: Via Bioconda (Recommended)

This installs scanexitron along with all required external compiled tools automatically:

conda install -c bioconda scanexitron

Option 2: Via PyPI

Installs the Python package. Note: You must install the external dependencies separately (see below).

pip install scanexitron

Option 3: From Source

git clone https://github.com/ylab-hi/ScanExitron.git
cd ScanExitron
pip install -e ".[dev]"

🛠️ External Dependencies

If you did not install via conda, make sure the following bioinformatics tools are installed and available on your system PATH:

📂 Reference Data Setup

Download your genome FASTA and matching transcript annotation files. For example, to setup hg38 reference resources:

# Download and decompress the hg38 genome
wget https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.fa.gz
gunzip hg38.fa.gz

# Download and decompress the Gencode release annotation
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/gencode.v37.annotation.gtf.gz
gunzip gencode.v37.annotation.gtf.gz

💻 Usage

🔍 1. Exitron Calling

Run scanexitron by pointing it to your reference FASTA, transcript annotation GTF, and the input BAM/CRAM file (which must have a .bai/.crai index file alongside it):

scanexitron run -i input.bam -r hg38.fa -g gencode.v37.annotation.gtf

Calling Options

🔄 2. Convert to VCF

Format your exitron tabular output into a standard VCF file using scanexitron convert:

scanexitron convert -i sample.exitron -r hg38.fa -o sample.vcf

VCF Converter Options

📊 Output Format

Results are written to <input>.exitron as a tab-delimited file with the following schema:

Note: RegTools intermediate files (<input>.janno) are preserved in the directory for manual inspection.

👩‍💻 Development

Contributions and local development setups are welcome:

# Install development and testing dependencies
pip install -e ".[dev]"

# Run test suite
pytest

📖 Citation

If you use ScanExitron in your research, please cite our papers:

• Molecular Cell: Molecular Cell Publication
• STAR Protocols: STAR Protocols Publication

📄 License

This project is licensed under the terms of the MIT License.

📬 Contact & Support

• Bug Reports & Feature Requests: Please submit an issue on the GitHub Issues tracker.