list_paired_fastq: Generate a list of paired fastq files from given directory.

In cb-42/cbmbtools: R Functions for Facilitating Microbiome Analyses

Description

Generate a list of paired fastq files from given directory.

Usage

list_paired_fastq(dir_in, f_out, mothur = TRUE)

Arguments

dir_in	Directory containing paired fastq files. Files that do not contain "_R1_" or "_R2_" in the filename will be ignored (e.g. config.xml).
f_out	Output file path. A .csv with two columns containing the fastq pairs listed in dir_in will be written to f_out.
mothur	Boolean for whether a fastq list is created for mothur processing (TRUE) or SRA upload preparation (FALSE). TRUE by default.

Value

No value is returned.

Examples

list_paired_fastq(dir_in = "unzipped_fastq_files_mothur", f_out = "miseq.txt")
list_paired_fastq(dir_in = "fastq_files_sra", f_out = "exp1_files.csv", mothur = FALSE)

cb-42/cbmbtools documentation built on Jan. 9, 2021, 1:38 a.m.