demultiplex {insect}

Demultiplex merged FASTQ

Description

This function is used to demultiplex FASTQ files containing sequence reads with index and primer sequences still attached. The function trims the tags and primers, and exports two FASTQ files for each forward-reverse index combination.

Usage

demultiplex(
  R1,
  R2 = NULL,
  tags,
  up,
  down,
  destdir = "demux",
  adapter1 = NULL,
  adapter2 = NULL
)

Arguments

R1

character string giving the path to the first FASTQ file

R2

character string giving the path to the second FASTQ file. Set to NULL for single-end reads.

tags

named character vector specifying the unique forward:reverse tag combinations used in the run. Each tag combination should be entered as an upper case character string delimited by a colon (e.g. "ATCGACAC:ATGCACTG") and named according to the unique sample ID.

up, down

upper case character strings giving the forward and reverse primer sequences.

destdir

character string giving the path to the directory where the new FASTQ files should be written.

adapter1

the forward flowcell adapter sequence to check and trim (set NULL to ignore). For standard Illumina MiSeq forward adapter set to "AATGATACGGCGACCACCGAGATCTACAC" (paired end sequencing only).

adapter2

the reverse flowcell adapter sequence to check and trim (set NULL to ignore). For standard Illumina MiSeq reverse adapter set to "CAAGCAGAAGACGGCATACGAGAT" (single or paired end sequencing).

Value

NULL (invisibly)

Author(s)

Shaun Wilkinson