simulateReads: Simulate reads from genome

Description Usage Arguments Details Value Author(s) Examples

View source: R/simulateReads.R

Description

Simulate single or paired end reads from any BSgenome-class object. These simulated reads can be mapped to the reference genome using any aligner to produce BAM files that can be used for mappability correction.

Usage

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simulateReads(bsgenome, readLength, bamfile, file,
  pairedEndFragmentLength = NULL, every.X.bp = 500)

Arguments

bsgenome

A BSgenome-class object containing the sequence of the reference genome.

readLength

The length in base pairs of the simulated reads that are written to file.

bamfile

A BAM file. This file is used to estimate the distribution of Phred quality scores.

file

The filename that is written to disk. The ending .fastq.gz will be appended.

pairedEndFragmentLength

If this option is specified, paired end reads with length readLength will be simulated coming from both ends of fragments of this size. NOT IMPLEMENTED YET.

every.X.bp

Stepsize for simulating reads. A read fragment will be simulated every X bp.

Details

Reads are simulated by splitting the genome into reads with the specified readLength.

Value

A fastq.gz file is written to disk.

Author(s)

Aaron Taudt

Examples

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## Get an example BAM file with single-cell-sequencing reads
bamfile <- system.file("extdata", "BB150803_IV_074.bam", package="AneuFinderData")
## Simulate 51bp reads for at a distance of every 5000bp
if (require(BSgenome.Mmusculus.UCSC.mm10)) {
simulateReads(BSgenome.Mmusculus.UCSC.mm10, bamfile=bamfile, readLength=51,
             file=tempfile(), every.X.bp=5000)
}

ataudt/aneufinder documentation built on Nov. 21, 2018, 10:10 a.m.