trim_fragments: Trims reads/fragments in fastqc files

View source: R/analysis.R

trim_fragmentsR Documentation

Trims reads/fragments in fastqc files

Description

This function takes a fastqc sequence and trims the reads returning a fastqc file with the trimmed reads.

Usage

trim_fragments(
  bin_path = "tools/fastx_toolkit/bin/fastx_trimmer",
  quality = 33,
  first_base = "",
  last_base = "",
  file_R1 = "",
  file_R2 = "",
  output_dir = "",
  verbose = FALSE
)

Arguments

quality

Min quality of reads to be trimmed.

first_base

First base to keep. Trims everything before this base.

last_base

Last base to keep. Trims everything after this base.

file_R1

Path to the input file with the sequence.

file_R2

Optional Path to the input with the reverse read sequence.

output_dir

Path to the output directory.

verbose

Enables progress messages. Default False.


TearsWillFall/DNAfrags documentation built on March 26, 2022, 6:02 a.m.