Generate paired-end FASTQ file

Simulates a paired-end FASTQ files from a genome and a gene annotation. The distribution of reads is randomly selected following a negative binomial distribution.

Usage

tx_generatePairedEndFASTQ(
  genome,
  geneAnnot,
  readLen_1,
  readLen_2,
  insertSize,
  libSize,
  fileName_r1,
  fileName_r2,
  TPM = NULL,
  NB_r = 5,
  NB_mu = 500,
  nCores
)

Arguments

genome

list. The full reference genome sequences, as loaded by tx_load_genome() or prepackaged by BSgenome, see ?BSgenome::available.genomes

geneAnnot

GRanges. Gene annotation as loaded by tx_load_bed().

readLen_1

integer. Length of simulated reads1

readLen_2

integer. Length of simulated reads2

insertSize

integer. Length of simulated insert (gap between reads)

libSize

integer. Size of simulated FASTQ file

fileName_r1

character. Name of output file reads1.

fileName_r2

character. Name of output file reads2.

TPM

numeric. Proportion of reads per gene in gene annotation. Overrides negative binomial distribution generation.

NB_r

numeric. Target r dispersion parameter. Bigger values of r tend to generate a normal distribution. See ?stats::rnbinom()

NB_mu

numeric. Target mean of the resulting distribution

nCores

integer. Number of cores to run the function with. Multicore capability not available in Windows OS.

Value

Writes FASTQ files fileName_r1 and fileName_r2