run_bedtools: Run the Bedtools program

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run the Bedtools program

Description

Runs the bedtools program

Usage

run_bedtools(
  command = NULL,
  input = NULL,
  reference = NULL,
  out.dir = NULL,
  sample.names = NULL,
  counts = NULL,
  name = NULL,
  strand = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  bedtools = NULL,
  version = FALSE
)

Arguments

command	Bedtools command to run, at present can only choose from 'coverage' or 'bamtobed'or "getfasta", required
input	List of aligned files in bam format, required
reference	GTF/GFF3 file for calculating the depth of coverage intervals
out.dir	Name of the directory from the Bedtools output
sample.names	List of sample names, required
counts	Only report the count of overlaps, default set to FALSE
name	Use the name field and coordinates for the FASTA header
strand	Force strandedness
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
bedtools	Path to the bedtools program, required
version	Returns the version number

Value

A list with the bedtools commands

Examples

## Not run: 
# Version
bedtools.path <- "/software/bedtools2/bin/bedtools"
bedtools.version <- run_bedtools(bedtools = bedtools.path,
                                 version = TRUE)

# Bedtools coverage
command = "coverage"
outputDirectory <- "coverage"
sam.files <- list.files(path = alignments.path, pattern = "sam$",
                        full.names = TRUE,
                        recursive = TRUE)
sorted.bam.files <- gsub(sam.files,
                         pattern = ".sam",
                         replacement = "_sorted.bam")
sample_names <- unlist(lapply(strsplit(list.files(path = reads_path,
                       pattern = "*_R1_001.fastq$",
                       full.names = FALSE),"_"), `[[`, 1))
gtfFile <- "mirBase/hsa.ensembl.gff3"

bedtools.cmds <- run_bedtools(command = command,
                              input = sorted.bam.files,
                              reference = gtfFile,
                              out.dir = outputDirectory,
                              sample.names = sample.names,
                              counts = TRUE,
                              bedtools = bedtools.path)
bedtools.cmds

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.