Wrapper function for fastq_quality_trimmer

fastq_quality_trimmer(
  fileTofqf,
  outFile = file.path(dirname(fileTofqf), paste0("QT_", basename(fileTofqf))),
  fqf = "fastq_quality_trimmer",
  qualityThreshold = 5,
  minimumLength = 20,
  qEncoding = 33,
  stderr = file.path(dirname(fileTofqf), paste0(basename(fileTofqf),
    "_fastq_quality_trimmer_stderr.txt")),
  stdout = file.path(dirname(fileTofqf), paste0(basename(fileTofqf),
    "_fastq_quality_trimmer_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE,
  writelog = T
)

Arguments

fileTofqf: path to file to process (fastq).
outFile: output file name.
fqf: path to fastq_quality_trimmer from FastX toolkit.
qualityThreshold: minimum quality score to keep.
minimumLength: minimum percent of bases that must have [-q] quality.
qEncoding: quality encoding, set to either 33 (Sanger Phred+33 encoding/Illumina fastq; default) or NULL (Phred+64 fastq).
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).
writelog: write stderr/stdout logs, TRUE (default) or FALSE.

Value

path to unzipped file

Author

Kathryn Rozen-Gagnon

Examples

 
testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile_FF <- ctk_fastqFilter(testFQ,qsFilter = "mean:0-29:20",verbose=TRUE)
#> fastq_filter.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl
#> fastq_filter.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl  -if sanger  -of fastq  -f mean:0-29:20  /Users/runner/work/_temp/Library/CLIPflexR/extdata/Fox3_Std_small.fq.gz  /Users/runner/work/_temp/Library/CLIPflexR/extdata/FF_Fox3_Std_small.fq.gz 
FqFile <- decompress(FqFile_FF,overwrite=TRUE)
FqFile_clipped <- fastx_clipper(FqFile,length=20)
FqFile_QF <- fastq_quality_trimmer(FqFile_clipped)