collapse.fastq {ORFik} | R Documentation

## Very fast fastq/fasta collapser

### Description

For each unique read in the file, collapse into 1 and state in the fasta header how many reads existed of that type. This is done after trimming usually, works best for reads < 50 read length. Not so effective for 150 bp length mRNA-seq etc.

### Usage

    collapse.fastq(
      files,
      outdir = file.path(dirname(files[1]), "collapsed"),
      header.out.format = "ribotoolkit",
      compress = FALSE,
      prefix = "collapsed_"
    )

### Arguments

`files` | paths to fasta / fastq files to collapse. I tries to detect format per file, if file does not have .fastq, .fastq.gz, .fq or fq.gz extensions, it will be treated as a .fasta file format.
`outdir` | outdir to save files, default: `file.path(dirname(files[1]), "collapsed")`. Inside same folder as input files, then create subfolder "collapsed", and add a prefix of "collapsed_" to the output names in that folder.
`header.out.format` | character, default "ribotoolkit", else must be "fastx". How the read header of the output fasta should be formated: ribotoolkit: ">seq1_x55", sequence 1 has 55 duplicated reads collapsed. fastx: ">1-55", sequence 1 has 55 duplicated reads collapsed
`compress` | logical, default FALSE
`prefix` | character, default "collapsed_" Prefix to name of output file.

### Value

invisible(NULL), files saved to disc in fasta format.

### Examples

    fastq.folder <- tempdir() # <- Your fastq files
    infiles <- dir(fastq.folder, "*.fastq", full.names = TRUE)
    # collapse.fastq(infiles)

[Package ORFik version 1.12.13 Index]