meta_demultiplex | R Documentation |
Function for demultiplexing sequencing reads arranged in a common format provided by sequencers (such as Illumina) generally for 16S data. This function takes a matrix of sample names/barcodes, a .fastq file of barcodes by sequence header, and a .fastq file of reads corresponding to the barcodes. Based on the barcodes given, the function extracts all reads for the indexed barcode and writes all the reads from that barcode to separate .fastq files.
meta_demultiplex(
barcodeFile,
indexFile,
readFile,
rcBarcodes = TRUE,
location = NULL,
threads = 1,
hammingDist = 0,
quiet = TRUE
)
barcodeFile |
Path to a file containing a .tsv matrix with a header row, and then sample names (column 1) and barcodes (column 2). |
indexFile |
Path to a .fastq file that contains the barcodes for
each read. The headers should be the same (and in the same order) as
|
readFile |
Path to the sequencing read .fastq file that corresponds
to the |
rcBarcodes |
Should the barcode indexes in the barcodeFile be reverse
complemented to match the sequences in the |
location |
A directory location to store the demultiplexed read files. Defaults to generate a new temporary directory. |
threads |
The number of threads to use for parallelization (BiocParallel). This function will parallelize over the barcodes and extract reads for each barcode separately and write them to separate demultiplexed files. |
hammingDist |
Uses a Hamming Distance or number of base differences to
allow for inexact matches for the barcodes/indexes. Defaults to |
quiet |
Turns off most messages. Default is |
Returns multiple .fastq files that contain all reads whose index matches the barcodes given. These files will be written to the location directory, and will be named based on the given sampleNames and barcodes, e.g. './demultiplex_fastq/SampleName1_GGAATTATCGGT.fastq.gz'
## Get barcode, index, and read data locations
barcodePath <- system.file("extdata", "barcodes.txt", package = "MetaScope")
indexPath <- system.file("extdata", "virus_example_index.fastq",
package = "MetaScope")
readPath <- system.file("extdata", "virus_example.fastq",
package = "MetaScope")
## Demultiplex
demult <- meta_demultiplex(barcodePath, indexPath, readPath, rcBarcodes = FALSE,
hammingDist = 2)
demult
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