tx_generateSingleEndFASTQ: Generate single-end FASTQ file

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

Generate single-end FASTQ file

Description

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

Usage

tx_generateSingleEndFASTQ(
  genome,
  geneAnnot,
  readLen,
  libSize,
  fileName,
  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	integer. Length of simulated reads
libSize	integer. Size of simulated FASTQ file
fileName	character. Name of output file.
TPM	numeric. Proportion of reads per gene in gene annotation
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 fileName

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