Question: Any Publicly Available Simulated Rna-Seq Dataset
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gravatar for narges
6.0 years ago by
narges180
Finland
narges180 wrote:

Hi,

I am testing a specific statistical approach for detecting DE genes in RNA-seq experiments. Right now I am working with real datasets which I precisely do not know about the number true positives. I know there are some methods to estimate the precision of the method, calculating the FPR and ... but can you recommend me any publicly available simulated dataset which is useful for my aim and I can use it as a control dataset for the method?

Thank you in advance

rnaseq dataset • 2.0k views
ADD COMMENTlink modified 6.0 years ago by polarise380 • written 6.0 years ago by narges180
2

See here, this has (almost...) already been answered before: Simulating RNA-seq reads However, I see you are looking for a published simulated dataset, not for a published tool to make simulated datasets.

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by Michael Dondrup46k

Thanks. Yes, actually now I am trying to make my own but I am also very interested in already available ones. Even actually it would be very nice to have spike in data in real biological datasets. An then the post you mentioned was a bit old I was wondering if any new issue has come during this period.

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by narges180
1
gravatar for polarise
6.0 years ago by
polarise380
Galway, Ireland
polarise380 wrote:

There are a lot of tools that one can use to generate synthetic reads. I've not come across any publicly available synthetic datasets. Here are some tools for simulating reads. Take your pick.

http://alumni.cs.ucr.edu/~liw/rnaseqreadsimulator.html

http://sammeth.net/confluence/display/SIM/Home (doi: 10.1093/nar/gks666)

http://useq.sourceforge.net/

ADD COMMENTlink written 6.0 years ago by polarise380
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