Use Rlsim With Empirical (Input) Expression Levels
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10.6 years ago
Rob 6.7k

I'm interested in simulating RNA-seq data using the rlsim tool. However, rather than randomly draw the expression levels from a mixture of distributions, I wish to control which transcripts are expressed at relative levels. Basically, I have an input distribution of relative abundances, and I want to simulate an RNA-seq dataset where these relative abundances are the underlying (latent) model parameters. Is this possible in rlsim? I wasn't able to find a way to do this by looking at the user manual. If it is possible, how would I accomplish it?

expression rna-seq simulation • 2.4k views
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10.5 years ago
Botond Sipos ★ 1.7k

rlsim cannot simulate from relative abundances (proportions) only, but you can easily "convert "the proportions to the absolute levels by multiplying them by a constant which is large enough for your purposes and then construct the input Fasta using those levels. You might have to play around with the multiplier using the -m flag, make sure that the "sampling ratio" reported by rlsim is small (let's say at least as small as 10^-5).

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That doesn't sound too difficult; thanks, Botond!

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Indeed it is not that difficult. Let me know if you bump into other obstacles.

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