Command line or python RNA-seq read simulator

Question

[i.sudbery]

Does anyone have any good recommendations for an RNA-seq read simulator, that will simulate raw RNA-seq reads from a transcript level quantification, that includes proper modelling of illumina error distributions and runs on the command line or in python. (I know about polyester, which is R based, but this is for an undergraduate student who doesn't know R and doesn't have time to learn).

If necessary I will write a wrapper for Polyester for them to use, but I'd rather I didn't have to take that solution.

[GenoMax]

Not python but randomreads.sh from BBMap may fit the bill.

[i.sudbery]

Do you know where I might find documation for this? I can't seem to find it on the main bbtools page?

[Brian Bushnell]

Note that if you want RNA-seq reads from randomreads you should use a transcriptome reference. Furthermore, add the "metagenome" flag, which despite the name, is described in the documentation as:

metagenome=f    Assign scaffolds a random exponential coverage level,
                to simulate a metagenomic or RNA coverage distribution.

Note that "metagenome=f" is the default (false) so to enable it you would add "metagenome" or "metagenome=t" which are equivalent.

[GenoMax]

If you run randomreads.sh without any options you will see extensive in-line help.

[i.sudbery]

Unforunately I don't see a way to simulate different expression levels for different transcripts in this script.

[Joe]

Can ART not do this?

[i.sudbery]

ART doesn't allow you to simulate different genes having different expression levels.

[GenoMax]

i.sudbery GPT came up with these options.

http://alumni.cs.ucr.edu/~liw/rnaseqreadsimulator.html
https://github.com/itmat/CAMPAREE

Both allow you to assign values to transcripts.

[i.sudbery]

rnaseqreadsimulator is python 2.7 and looks long unmaintained. CAMPAREE looks more promising, but the documentation is lacking, and neither I nor the student have time to be working out how it works.