mergeFastq {ORFik} | R Documentation |
Will use multithreading to speed up process. Only works for Unix OS (Linux and Mac)
mergeFastq(in_files, out_files, BPPARAM = bpparam())
in_files |
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out_files |
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BPPARAM |
how many cores/threads to use? default: bpparam().
To see number of threads used, do |
invisible(NULL).
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)