prepare_reads {demulticoder}R Documentation

Prepare reads for primer trimming using 'Cutadapt'

Description

Prepare reads for primer trimming using 'Cutadapt'

Usage

prepare_reads(
  data_directory = "data",
  output_directory = tempdir(),
  tempdir_path = NULL,
  tempdir_id = "demulticoder_run",
  overwrite_existing = FALSE
)

Arguments

data_directory

Directory path where the user has placed raw FASTQ (forward and reverse reads), metadata.csv, and primerinfo_params.csv files. Default is "data".

output_directory

User-specified directory for outputs. Default is tempdir().

tempdir_path

Path to a temporary directory. If NULL, a temporary directory path will be identified using the tempdir() command.

tempdir_id

ID for temporary directories. The user can provide any helpful ID, whether it be a date or specific name for the run. Default is "demulticoder_run"

overwrite_existing

Logical, indicating whether to remove or overwrite existing files and directories from previous runs. Default is FALSE.

Value

A list containing data tables, including metadata, primer sequences to search for based on orientation, paths for trimming reads, and user-defined parameters for all subsequent steps.

Examples


# Pre-filter raw reads and parse metadata and primer_information to prepare
# for primer trimming and filter
analysis_setup <- prepare_reads(
  data_directory = system.file("extdata", package = "demulticoder"),
  output_directory = tempdir(),
  overwrite_existing = TRUE
)


[Package demulticoder version 0.1.2 Index]