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 |
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 |
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
)