Hi All,

Do you know of a software package to generate simulated data of RNA-seq reads? And I mean the reads themselves, not read counts. My goal is to do some benchmarking on RNA-seq methods.

Quick google-fu found me rlsim: https://www.ebi.ac.uk/goldman-srv/rlsim/. But the latest version of rlsim is 2014. And the corresponding paper seems to be a BioRxiv article from 2015... which seemingly has never been published.

Thank you in advance.

RM

A Google search for RNA read simulation led me to the Bioconductor polyester package, which was #4 on my list of hits.

We recently developed simReads in the Rsubread package, because the limited existing options all seemed to me to be relatively slow and hard to use. The R-based options in particular use so much memory that we found they could be used only for very small simulations.