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)
}