ScanExitron

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A computational workflow for exitron splicing identification

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# ScanExitron

<p align="center">
  <strong>A computational workflow for exitron splicing identification from RNA-Seq data.</strong>
</p>

---

## 🌟 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:
```bash
conda install -c bioconda scanexitron
```

### Option 2: Via PyPI
Installs the Python package. *Note: You must install the external dependencies separately (see below).*
```bash
pip install scanexitron
```

### Option 3: From Source
```bash
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:

```bash
# 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):

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

---

### 🔄 2. Convert to VCF
Format your exitron tabular output into a standard VCF file using `scanexitron convert`:

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

---

## 📊 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:

```bash
# 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](https://www.sciencedirect.com/science/article/pii/S1097276521002239)
* **STAR Protocols**: [STAR Protocols Publication](https://star-protocols.cell.com/protocols/977)

---

## 📄 License

This project is licensed under the terms of the **[MIT License](https://github.com/ylab-hi/ScanExitron/blob/main/LICENSE)**.

---

## 📬 Contact & Support

- **Bug Reports & Feature Requests**: Please submit an issue on the [GitHub Issues tracker](https://github.com/ylab-hi/ScanExitron/issues).

ScanExitron

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