tx_generatePairedEndFASTQ: Generate paired-end FASTQ file

In AngelCampos/txtools: An R package facilitating analysis of RNA modifications, structures, and interactions

Generate paired-end FASTQ file

Description

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

AngelCampos/txtools documentation built on Sept. 16, 2024, 10:25 p.m.