Quick Start

Get ORILINX running in 5 minutes.

Installation

Install from PyPI:

pip install orilinx
orilinx fetch_models

Or install from source:

git clone https://github.com/Pfuderer/ORILINX.git
cd ORILINX
pip install -e .
orilinx fetch_models

ORILINX includes a pre-trained model. The fetch_models command downloads the required weights (~900 MB).

Get a genome

Download the human genome (hg38) from UCSC:

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
gunzip hg38.fa.gz

Make a prediction

Predict replication origins on a 4 Mb region of chromosome 8:

orilinx --fasta_path hg38.fa --output_dir orilinx_results --sequence_names chr8:1000000-5000000

The results appear in a new orilinx_results/ folder as chr8.bedGraph.

That’s it! The file contains shows the probability that each 2000 bp window in this region is a replication origin.

What next?