fastq_quality_filter: Wrapper function for fastq_quality_filter

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for fastq_quality_filter

Description

Wrapper function for fastq_quality_filter

Usage

fastq_quality_filter(
  fileTofqf,
  outFile = file.path(dirname(fileTofqf), paste0("QF_", basename(fileTofqf))),
  fqf = "fastq_quality_filter",
  qEncoding = 33,
  minimumQuality = 20,
  minimumPercentOfRead = 80,
  stderr = file.path(dirname(fileTofqf), paste0(basename(fileTofqf),
    "_fastq_quality_filter_stderr.txt")),
  stdout = file.path(dirname(fileTofqf), paste0(basename(fileTofqf),
    "_fastq_quality_filter_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_filter from FastX toolkit.
qEncoding	quality encoding, set to either 33 (Sanger Phred+33 encoding/Illumina fastq; default) or NULL (Phred+64 fastq).
minimumQuality	minimum quality score to keep (default is 20).
minimumPercentOfRead	minimum percent of bases that must have [-q] quality (default is 80).
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(s)

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)
FqFile <- decompress(FqFile_FF,overwrite=TRUE)
FqFile_clipped <- fastx_clipper(FqFile,length=20)
FqFile_QF <- fastq_quality_filter(FqFile)

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.