Demultiplex and tag fastq files using sample barcodes

Source: R/AllGenerics.R, R/demultiplexFASTQ.R

Demultiplex and tag fastq files using sample barcodes

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

# S4 method for 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()
#> Checking de-multiplexed R1 reads
#> Checking de-multiplexed R2 reads
#> Checking mapped file
#> Checking de-duplicated file

# demultiplex allowing one mismatch in sample indexes
dir.create("demult_fastq")
#> Warning: 'demult_fastq' already exists
cs <- demultiplexFASTQ(cs, outdir =  "demult_fastq", max_mismatch = 1)
#> de-multiplexing the FASTQ file
#> Warning: Output files already exist! Overwriting..
#> Warning: Output files already exist! Overwriting..
#> Warning: Output files already exist! Overwriting..
#> Warning: Output files already exist! Overwriting..