mnase_classifier

A detailed description of this project can be found here

Requirements

It is strongly recommended to sort the BAM files by name before running this tool.

samtools sort -n -o output.bam input.bam

Getting started

Getting the project up and running is as simple as:

Install from pypi

pipx install mnase-classifier

Install from source

if you want to install it from source you will need uv installed

clone the repository

git clone git@gitbio.ens-lyon.fr:LBMC/Bernard/mnase_classifier.git
cd mnase_classifier

Initialize the uv environment:

uv sync

Print help:

uv run mnase_classifier --help

Usage example

Classify paired reads from a BAM file into groups based on insert size:

uv run mnase_classifier --bam_input path/to/file.bam --outdir outdir --means "110 150 250 300" --min --max -v 

The -v flag enables verbose output for debugging.