Cool - that's what I had kinda thought, thanks for replying Rob
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rsem-simulate-reads: simulating different data
I'm using RSEM to simulate reads from previous experiments (rsem-simulate-reads) - I have no problems getting the basics working, but having difficulties adjusting simulation based params.
Here's an example:
- Use RSEM to prepare reference (bowtie2 or STAR)
rsem-prepare-reference - Calculate expression
rsem-calculate-expression - Then simulate reads:
rsem-simulate-readswith something similar to this:
rsem-simulate-reads Human_ref/ref expression/results.stat/results.model \
expression/results.isoforms.results 0.1 500000 simulation/sim_data
The original data is PE, 150bp, non-stranded, bulk RNA-seq
From what I can gather, it is possible to adjust the model params (https://github.com/deweylab/RSEM/blob/master/model_file_description.txt) to simulate new reads with different library options. For example, say I wanted 50bp PE reads, or 50bp SE stranded reads.
Is this possible using RSEM? I know this is possible using Polyester (https://bioconductor.org/packages/release/bioc/vignettes/polyester/inst/doc/polyester.html), which I'm using, but was hoping to use RSEM as well.
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jiangminghao1001 •
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reganhayward •
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reganhayward •
1 answer
The parameters in the RSEM model file are learned by the quantifier on an experimental data set. Since parameters will differ (possibly drastically) between a 150bp PE dataset and a 50bp SE dataset, its not possible to directly use one model's parameters to simulate a dataset with different characteristics. You could always spoof the parameters, or try to set them according to a parametric model, the resulting data may then not be a good match for a specific experimental dataset.
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hello, I’d like to simulate reads from the model file generated by rsem-calculate-expression function from a pair-end data. However, the rsem-simulate-reads always output one .fa file.
I replace the model file and the isoform_results file with other random files, but the simulate function still worked and one .fa file was generated.
Here is what I did:
Did I utilise the function wrongly? I’ll appreciate if you could give me some instructions. Thank you very much!