iRRBS 0.1.0

RRBS tool for deleting artificial cytosins

# 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