offsetATAC: Offset correction for ATAC-seq data

In mireia-bioinfo/pipelineNGS: Methods for Epigenetic Data Processing

Offset correction for ATAC-seq data

Description

It performs the offset correction needed for ATAC-seq data: +4bp in forward strand; -5bp in reverse strand.

Usage

offsetATAC(file, cores = 6, gen_sizes = "/vault/refs/hg38.chromSizes.txt")

Arguments

file	Character string with the filename and path for the BAM file.
cores	Number of threads to use for the analysis.
gen_sizes	Character string indicating the path where the file with chromosome name and sizes can be found. This argument is necessary only when type="SE".

Value

Returns the final BAM file, sorted and indexed, in path_bam.

Examples

## Not run: 
offsetATAC(file)

## End(Not run)

mireia-bioinfo/pipelineNGS documentation built on Jan. 2, 2023, 11:18 a.m.