JuncSeq

JuncSeq is a bioinformatics tool designed to detect and analyse aberrant splicing events using splice junction data. It enables researchers to:

1. Identify aberrant splicing in a predefined list of genes.
2. Detect splice junction abnormalities near specific genetic variants.

Installation

You can install JuncSeek directly from GitHub:

pip install git+https://github.com/CCICB/juncseek.git

Alternatively, you can clone the repository and install it in editable mode:

git clone https://github.com/CCICB/juncseek.git
cd juncseek
pip install --editable .

Usage

Once installed, you can run juncseek from the command line as follows:

juncseek [-h] --patient-list PATIENT_LIST --gtf GTF [--gene-list GENE_LIST] [--vcf VCF] --output OUTPUT

Arguments:

• --patient-list PATIENT_LIST : Path to the patient list file (only needs paths as input).
• --gtf GTF : Path to the GTF annotation file.
• --gene-list GENE_LIST (optional) : Path to the gene list file.
• --vcf VCF (optional) : Path to the VCF file containing variant data.
• --output OUTPUT : Path to the output directory.