FastQ rather than fasta RNA-Seq read simulation

Question

[GLR]

Hi all,

I've been using polyester to simulate RNA-Seq reads with great success, but I was hoping to be able to simulate some RNA-Seq fastq reads and polyester only seems to be able to output fasta files. Does anyone know of any way I can generate some qual files to alongside these simulated datasets? I know most aligners can run with fasta files, but I was hoping to play around with kallisto and the documentation for this details the input as fastq and there doesn't seem to be an optional fasta flag as there is with some alignment tools.

Thank you!

Answer 1

[Gordon Smyth]

The Bioconductor function Rsubread::simReads does that.

[GLR]

Thank you so much, I'll give that a look.