RunTrimGalore: R interface to TrimGalore please see TrimGalore web site at...

In elmerfer/RAPInetMHCpan: an R API to netMHCpan and netMHCIIpan softwares for neural network prediction of peptide binders

Description

R interface to TrimGalore please see TrimGalore web site at https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md

Usage

RunTrimGalore(
  file,
  paired = TRUE,
  quality = 20,
  phred33 = TRUE,
  phred64 = FALSE,
  fastqc = FALSE,
  max_length,
  error_rate = 0.1,
  gzip = TRUE,
  length = 20,
  maxn,
  trimn,
  outdir,
  report_file = TRUE,
  clip_R1,
  clip_R2,
  three_prime_clip_R1,
  three_prime_clip_R2,
  retain_unpaired,
  length_1 = 35,
  length_2 = 35,
  trim1,
  cores = 4,
  remove_intermediate = paired
)

Arguments

file	a character vector with the file names or the files names to be processed. The fasts should end in .fastq
quality	(integer>0) see –quality at TrimGalore web site
phred33	(logical) if TRUE, then –phred33 ON, else –phred33 OFF (see at TrimGalore web site)
phred64	(logical) (see –phred64 at TrimGalore web site)
max_length	(integer) (see –max_length at TrimGalore web site)
error_rate	(float) default 0.1 (see -e option at TrimGalore web site)
gzip	(logical) if TRUE (default) the output files will be zipped (see–gzip and –dont_zip at TrimGalore web site)
length	(integer) default 20 (see –length at TrimaGalore web site)
maxn	(integer) (see –max_n at TrimGalore web site)
trimn	(integer) (see –trim-n at TrimGalore web site)
outdir	(character) if missing the output will be stored at the same directory of the (first) input file. (see –output_dir at TrimGalore web site)
report_file	(logical) (default TRUE) (see –repot_file at TrimGalore web site)
clip_R1	(integer) (see –clip_R1 at TrimGalore web site)
clip_R2	(integer) (see –clip_R2 at TrimGalore web site)
three_prime_clip_R1	(see –three_prime_clip_R1 at TrimGalore web site)
three_prime_clip_R2	(see –three_prime_clip_R2 at TrimGalore web site)
retain_unpaired	(see –retain_unpaired at TrimGalore web site)
length_1	(integer) default 35) (see –length_1 at TrimGalore web site)
length_2	(integer) default 35) (see –length_2 at TrimGalore web site)
trim1	(integer) (see –trim1 at TrimGalore web site)
cores	( integer) (default 4) number of cores or threads to use (see –cores at TrimGalore web site)
remove_intermediate	remove intermediate trimmed files (only fif paired == TRUE)
pared	(TRUE default) if paired == TRUE, the it will look for the second fastq file for each file. The files are expected to be .fastq and identified as XXXX_1.fastq and their corresponding pair XXXX_2.fastq.
fasqc	(logical) if TRUE will run fastqc in its default version

Details

see output files definitions at TrimGalore web site

Value

none

Author(s)

Elmer A. Fernández

elmerfer/RAPInetMHCpan documentation built on Sept. 17, 2021, 2:14 p.m.