get_fragment_length_bed: Extract fragment length from a BAM file.

In TearsWillFall/DNAfrags: Filter DNA fragments in BAM files by length and location

Extract fragment length from a BAM file.

Description

This function takes a BAM file and a BED file as an input and outputs the fragment length distributions of all the regions in a TXT file.

Usage

get_fragment_length_bed(
  bin_path = "tools/samtools/samtools",
  bam = "",
  bed = "",
  max_frag_length = 1000,
  mapq = 10,
  threads = 1,
  output_dir = "",
  verbose = FALSE,
  mode = 0,
  start = NULL,
  end = NULL,
  start_bin = NULL,
  end_bin = NULL
)

Arguments

bin_path	Path to samtools executable. Default path tools/samtools/samtools.
bam	Path to BAM file.
bed	Path to BED file.
max_frag_length	Maximum fragment length to keep. Default 1000.
mapq	Minimum MapQ of the reads to keep. Default 10.
threads	Number of cores. Default 1
output_dir	Directory to output results.
verbose	Enables progress messages. Default False.
mode	Mode in which to output the fragment length. Default 0. Mode 0: Returns fragment length for R1 and R2 reads. Mode 1: Returns fragment legnth for R1 reads. Mode 2: Returns fragment length for R2 reads.
start	Downstream distance from (start+end)/2 position in bed file
end	Upstream distance from (start+end)/2 position in bed file
start_bin	Downstream distance from (start+end)/2 position in bed file for bin
end_bin	Upstream distance from (start+end)/2 position in bed file for bin

TearsWillFall/DNAfrags documentation built on March 26, 2022, 6:02 a.m.