get_coverage_bed: Get coverage for target regions

In TearsWillFall/tfProfiling: An implementation of PeterUlz (https://github.com/PeterUlz/TranscriptionFactorProfiling) TranscriptionFactorProfiling pipeline in R for GNU/Unix based systems

Description

This function takes a BAM and a BED file with target regions and estimate per base coverage for them using samtools depth

Usage

get_coverage_bed(
  bin_path = "tools/samtools/samtools",
  bam = "",
  bed = "",
  mapq = 0,
  threads = 3,
  output_dir = ""
)

Arguments

bin_path	Path to samtools. Default tools/samtools/samtools
bam	Path to BAM file
bed	Path to BED file
mapq	Minimum mapping quality
threads	Number of threads to use. Default 3
output_dir	Directory to output results

Value

A double with the mean genome coverage

TearsWillFall/tfProfiling documentation built on Aug. 7, 2021, 9:40 a.m.