metaloops-25

This repository aims to facilitate the conversion of Hi-C data formats h5, bedpe and cool into mcool, which can be used to run metaloops for loop calling. These conversion scripts are located in Conversion_scripts.

Installation

To install the pipeline clone the repository:

git clone https://github.com/ccarloscr/metaloops-25
cd metaloops-25

Metaloops and conversion scripts require python3, hdf5plugin, h5py, numpy, cooler, R (v4) and multiple R packages. These programs are detailed in the environment.yml file provided.

Create a conda environment named workplace using the provided environment.yml:

conda env create -f env.yml

Additionally, the conversion of bedpe files into cool requires a chrom.sizes .txt file indicating the size of each chromosome. The Drosophila dm6 chrom.sizes file is included in the repository.

Configuration

The scripts on this reposition are configured to run using SLURM. Change the scripts' headers according to your preferred job manager.

Credits

This project uses the script metaloops.sh developed by Julien Dorier and the Lausanne University, available under license GNU GPLv3. The original repository can be found in [meta-loops-2022].