read_fastq {demulticoder}R Documentation

Takes in the FASTQ files from the user and creates a data.frame with the paths to files that will be created and used in the future. Included in a larger 'read_prefilt_fastq' function.

Description

Takes in the FASTQ files from the user and creates a data.frame with the paths to files that will be created and used in the future. Included in a larger 'read_prefilt_fastq' function.

Usage

read_fastq(data_directory_path, temp_directory_path)

Arguments

data_directory_path

The path to the directory containing raw FASTQ (forward and reverse reads), metadata.csv, and primerinfo_params.csv files.

temp_directory_path

User-defined temporary directory to output unfiltered, trimmed, and filtered read directories throughout the workflow.

Value

A data.frame with the FASTQ file paths, primer orientations and sequences, and parsed sample names.


[Package demulticoder version 0.1.2 Index]