Split multiplexed samples by user-defined indics using fastx_barcode_splitter

fastx_barcode_splitter(
  fileTofxc,
  bcFile,
  mismatches = 0,
  fbs = "fastx_barcode_splitter.pl",
  stderr = file.path(dirname(fileTofxc), paste0(basename(fileTofxc),
    "_fastx_barcode_splitter_stderr.txt")),
  stdout = file.path(dirname(fileTofxc), paste0(basename(fileTofxc),
    "_fastx_barcode_splitter_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE
)

Arguments

fileTofxc

path to file to process (fastq or fasta).

bcFile

tab-delimited barcode file.

mismatches

number of mismatches allowed.

fbs

path to fastx_barcode_splitter.pl from FASTX toolkit.

stderr

path to stderr file.

stdout

path to stdout file.

useClipRConda

use conda environment installed by Herper, TRUE (default) or FALSE.

additional_Args

additional arguments to be passed to system call.

verbose

print messages to screen, TRUE or FALSE (default).

Value

path to split files; files will be written without any extension, in the same format as the input file.

Author

Kathryn Rozen-Gagnon