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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

if (FALSE) {
offsetATAC(file)
}