mergeFastq {ORFik} | R Documentation

## Merge groups of Fastq /Fasta files

### Description

Will use multithreading to speed up process. Only works for Unix OS (Linux and Mac)

### Usage

    mergeFastq(in_files, out_files, BPPARAM = bpparam())

### Arguments

`in_files` | `character` specify the full path to the individual fastq.gz files. Seperated by space per file in group: For 2 output files from 4 input files: in_files <- c("file1.fastq file2.fastq". "file3.fastq file4.fastq")
`out_files` | `character` specify the path to the FASTQ directory For 2 output files: out_files <- c("/merged/file1&2.fastq", "/merged/file3&4.fastq")
`BPPARAM` | how many cores/threads to use? default: bpparam(). To see number of threads used, do `bpparam()$workers`

### Value

invisible(NULL).

### Examples

    fastq.folder <- tempdir() # <- Your fastq files
    infiles <- dir(fastq.folder, "*.fastq", full.names = TRUE)
    ## Not run:
    # Seperate files into groups (here it is 4 output files from 12 input files)
    in_files <- c(paste0(grep(infiles, pattern = paste0("ribopool-",
                   seq(11, 14), collapse = "|"), value = TRUE), collapse = " "),
                  paste0(grep(infiles, pattern = paste0("ribopool-",
                   seq(18, 19), collapse = "|"), value = TRUE), collapse = " "),
                  paste0(grep(infiles, pattern = paste0("C11-",
                   seq(11, 14), collapse = "|"), value = TRUE), collapse = " "),
                  paste0(grep(infiles, pattern = paste0("C11-",
                   seq(18, 19), collapse = "|"), value = TRUE), collapse = " "))

    out_files <- paste0(c("SSU_ribopool", "LSU_ribopool", "SSU_WT", "LSU_WT"), ".fastq.gz")
    merged.fastq.folder <- file.path(fastq.folder, "merged/")
    out_files <- file.path(merged.fastq.folder, out_files)

    mergeFastq(in_files, out_files)

    ## End(Not run)

[Package ORFik version 1.12.13 Index]