Splits FASTQ files into individual samples.

This function will take each of the sequences barcodes and tries to find the corresponding barcode from the reference set. After that it writes new fastq files containing only the reads for a single barcode.

split_barcodes(reads, index, out, ref, n = 1e+05, max_ed = 1)

Arguments

reads

A character vector containing the read files in fastq format.
index

The index file containing the demultiplexed barcodes for each read file.
out

A folder to which to save the split fastq files.
ref

A character vector or DNAStringSet containing the reference barcodes.
n

Maximum number of records to read in each iteration.
max_ed

Maximum allowed edit distance between the sequenced and reference barcode.

Value

A numeric vector containing three entries, where the first defines the reads that are kept.

  • The number of reads that could be mapped uniquely.

  • The number of reads for which no match was found.

  • The number of reads for which more than one reference match was found.

Examples

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#> NULL