run_trimmomatic: This function uses trimmomatic to trim input fastq files and...

In uashogeschoolutrecht/structural_colours: Package For Project Structural Colour

Description

This function uses trimmomatic to trim input fastq files and outputs them to the specified base dir. Please supply input as character type.

Usage

run_trimmomatic(
  mode = "SE",
  f1,
  f2 = "",
  prefix = "trimmed",
  phred = "33",
  minlen = "90",
  window = "4:15",
  logfile = "trimmomatic_log.txt"
)

Arguments

mode	Single end ("SE") or paired end ("PE") fastq file(s) input, default = "SE"
f1	Absolute path to fastq read one, supply single end file / direction one PE here
f2	Absolute path to fastq read two, only use for second paired end file not for single end file, default = "". (single end)
prefix	Name of prefix for output files. Default = "trimmed"
phred	Phred scale, e.g. 33 / 64. Default = "33"
minlen	Minimum length of reads to keep, default = "90"
window	Sliding window for quality trimming to use, default = "4:15"
outdir	Absolute path directory to store output files, default = "./trimmomatic". Directory will be made my script.

Value

Creates trimming output files in specified directory

uashogeschoolutrecht/structural_colours documentation built on June 20, 2020, 4:07 p.m.