Command line or python RNA-seq read simulator
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3 months ago

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.

simulation RNA-seq • 780 views
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Not python but randomreads.sh from BBMap may fit the bill.

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

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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.

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

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

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Can ART not do this?

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

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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.

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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.

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