simulateReads: Simulate reads from genome
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description Usage Arguments Details Value Author(s) Examples

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.

1 2	simulateReads(bsgenome, readLength, bamfile, file, pairedEndFragmentLength = NULL, every.X.bp = 500)

`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.

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

A fastq.gz file is written to disk.

Aaron Taudt

## 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)
}