run_umitools: Run UMITools

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

Run UMITools

Description

UMITools are a set of tools for dealing with Unique Molecular Identifiers. Runs the commands extract and dedup.

Usage

run_umitools(
  command = NULL,
  input1 = NULL,
  input2 = NULL,
  output1 = NULL,
  output2 = NULL,
  log.file.names = NULL,
  umi.pattern = NULL,
  umi.position = NULL,
  three.prime = FALSE,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  umitools = NULL,
  version = FALSE
)

Arguments

command	Umitools command
input1	List of the paths to files containing to the forward reads
input2	List of the paths to files containing to the reverse reads
output1	List of paths to the files to write the processed forward reads
output2	List of paths to the files to write the processed reverse reads
log.file.names	List of paths to write log file to
umi.pattern	Barcode/UMI pattern, N = UMI position (required), C = cell barcode position (optional), X = sample position (optional)
umi.position	Read with the UMI, forward or reverse
three.prime	Barcode/UMI at 3' end of read
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
umitools	Path to the Umitools program, required
version	Returns the version number

Value

A file with the Umitools commands

Examples

 ## Not run: 
 # Version number
 umitools.path <- "/software/anaconda3/bin/umi_tools"

 run_umitools(umitools = umitools.path,
              version = TRUE)

 run_umitools(command = "extract",
              input1 = "reads1.fq",
              input2 = "reads2.fq",
              output1 = "umi.reads1.fq",
              output2 = "umi.reads2.fq",
              umi.pattern = "NNNNNNNN",
              umi.position = "reverse",
              execute = FALSE,
              umitools = umitools.path)

 run_umitools(command = "dedup",
              input1 = "align.bam",
              output1 = "dedup.align.bam",
              log.file.names = "align1",
              execute = FALSE,
              umitools = umitools.path)

## End(Not run)

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