writeReads: Create fastq file from read positions
In ChIPsim: Simulation of ChIP-seq experiments

Description Usage Arguments Details Value Author(s) See Also

This is an interface to pos2fastq that writes all reads for a given genome to a single file.

1	writeReads(readPos, readNames, sequence, quality, file, ...)

`readPos`	List of read positions with each component holding the read positions for one chromosome, which are themselves two component lists that provide forward and reverse strand positions.
`readNames`	List of the same shape as `readPos` providing read names.
`sequence`	Genome reference sequence (a `DNAStringSet`).
`quality`	Read quality scores (see Details).
`file`	Output file.
`...`	Further arguments to `pos2fastq`.

If quality looks like it might refer to a fastq file an attempt is made to create a ShortReadQ object. The read qualities of any ShortReadQ object passed as quality (directly or indirectly as file name) are extracted and passed on to pos2fastq as quality argument. Otherwise it is passed on unchanged.

The name of the output file.

Peter Humburg

pos2fastq

ChIPsim documentation built on Nov. 8, 2020, 8:09 p.m.