demultiplexFASTQ {icetea} | R Documentation

## Demultiplex and tag fastq files using sample barcodes

### Description

Demultiplex and tag fastq files using sample barcodes

### Usage

    demultiplexFASTQ(CSobject, outdir, max_mismatch = 0, ncores = 1)

    ## S4 method for signature 'CapSet'
    demultiplexFASTQ(CSobject, outdir, max_mismatch = 0, ncores = 1)

### Arguments

`CSobject` | CapSet object created using `newCapSet` function
`outdir` | character. path to output directory
`max_mismatch` | integer. maximum allowed mismatches in the sample barcode
`ncores` | integrer. No. of cores/threads to use

### Value

de-multiplxed fastq files corresponding to each barcode. The files are written on disk with the corresponding sample names as specified in the CapSet object

### Examples

    # load a previously saved CapSet object
    cs <- exampleCSobject()

    # demultiplex allowing one mismatch in sample indexes
    dir.create("demult_fastq")
    cs <- demultiplexFASTQ(cs, outdir =  "demult_fastq", max_mismatch = 1)

[Package icetea version 1.8.0 Index]