Metadata-Version: 2.1
Name: iRRBS
Version: 0.1.0
Summary: RRBS tool for deleting artificial cytosins
Home-page: https://github.com/fothia/iRRBS
Author: Abel Fothi
Author-email: fothi.abel@gmail.com
License: MIT
Download-URL: https://github.com/fothia/iRRBS/archive/refs/tags/0.1.0.tar.gz
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: Unix
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
License-File: LICENSE

# iRRBS
# iRRBS tool
## Overview
3’ ends of RRBS reads overlapping with genomic MspI sites include non-methylated cytosines introduced through end-repair. These cytosines are not recognized by Trim Galore and are therefore not trimmed but considered during methylation calling. To avoid methylation bias we developed iRRBS, which identifies and hides end-repaired cytosines from methylation calling.

## Features
- Detecting whether the input file is single-read or paired-end
- Logging the "Number of unique MspI reads", the "Number of MspI reads" and the "Number of all reads"
- Outputting a BAM file without the biased cytosines


## Usage
To run iRRBS the following input parameters are required in this order:
- infile: path to input sorted BAM file
- chromsizes: path to chrom.sizes file to define the chromosome lengths for a given genome
- genome: path to genome file
-outfile: name for the output file

## Dependencies
- samtools
- bedtools


