count_genome_cuts: Counts DNase-seq or ATAC-seq cuts along the genome

In HarteminkLab/TOP: Predict transcription factor occupancy using DNase- or ATAC-seq data

Counts DNase-seq or ATAC-seq cuts along the genome

Description

Counts genomic cuts (5' end) from DNase-seq or ATAC-seq BAM alignment files using bedtools For ATAC-seq, when shift_ATAC = TRUE, shifts reads so as to address offsets and align the signal across strands.

Usage

count_genome_cuts(
  bam_file,
  chrom_size_file,
  data_type = c("DNase", "ATAC"),
  shift_ATAC = TRUE,
  shift_ATAC_bases = c(4L, -4L),
  outdir = dirname(bam_file),
  outname,
  bedtools_path = "bedtools",
  bedGraphToBigWig_path = "bedGraphToBigWig"
)

Arguments

bam_file	Sorted BAM file.
chrom_size_file	Chromosome size file.
data_type	Data type. Options: ‘DNase’ or ‘ATAC’.
shift_ATAC	Logical. When shift_ATAC=TRUE (and data_type='ATAC'), shifts reads according to shift_ATAC_bases.
shift_ATAC_bases	Number of bases to shift on + and - strands. Default: shifts reads on + strand by 4 bp and reads on - strand by -4 bp.
outdir	Output directory (default: use the directory of bam_file).
outname	Output prefix (default: use the prefix of bam_file).
bedtools_path	Path to bedtools executable.' (default: 'bedtools')
bedGraphToBigWig_path	Path to UCSC bedGraphToBigWig executable. (default: 'bedGraphToBigWig')

Examples

## Not run: 
# ATAC-seq data
count_genome_cuts(bam_file='K562.ATAC.bam',
                  chrom_size_file='hg38.chrom.sizes',
                  data_type='ATAC',
                  shift_ATAC=TRUE,
                  outdir='processed_data',
                  outname='K562.ATAC')

# DNase-seq data
count_genome_cuts(bam_file='K562.DNase.bam',
                  chrom_size_file='hg38.chrom.sizes',
                  data_type='DNase',
                  outdir='processed_data',
                  outname='K562.DNase')

## End(Not run)

HarteminkLab/TOP documentation built on July 27, 2023, 6:14 p.m.