setFastPrimerTrim: Create a fastPrimerTrim object Users have the option of...

In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses

Description

Create a fastPrimerTrim object Users have the option of trimming adapters from their data using bbduk.sh

Usage

setFastPrimerTrim(
  inDir,
  outDir,
  adapterList,
  paired = FALSE,
  validate = FALSE,
  maxMismatch = 2,
  allowIndels = FALSE,
  trimF = FALSE,
  trimR = FALSE,
  orient = FALSE,
  compress = FALSE
)

Arguments

inDir	Required input. Path to directory containing FASTQ files.
outDir	Required input. Path to write output files.
adapterList	Required input. List of adapter sequences to remove from files.
paired	Default is FALSE. When TRUE, two adapter sequences will be expected in file listed in "listOfAdapters"
validate	Default is FALSE. When TRUE, all validation method are executed.
maxMismatch	Default is 2. Sets the number of bases to mismatch when aligning forward / reverse adapters to sequences.
allowIndels	Default is false. Allows gaps / insertions when aligning forward / reverse adapters to sequences.
trimF	Default is FALSE. Trim forward reads.
trimR	Default is FALSE. Trim reverse reads.
orient	Default is FALSE. Orient forward and reverse reads into the same direction
compress	Default is FALSE. When TRUE, all output files are gzipped. TODO: Add Example

ananata/fastq2otu documentation built on Feb. 2, 2022, 4:20 p.m.