trim_fragments: Trims reads/fragments in fastqc files

In TearsWillFall/DNAfrags: Filter DNA fragments in BAM files by length and location

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.