Question: Use Rlsim With Empirical (Input) Expression Levels
1
gravatar for Rob
6.4 years ago by
Rob3.7k
United States
Rob3.7k wrote:

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?

simulation expression rna-seq • 1.6k views
ADD COMMENTlink modified 6.4 years ago by Botond Sipos1.7k • written 6.4 years ago by Rob3.7k
0
gravatar for Botond Sipos
6.4 years ago by
Botond Sipos1.7k
United Kingdom
Botond Sipos1.7k wrote:

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).

ADD COMMENTlink written 6.4 years ago by Botond Sipos1.7k

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

ADD REPLYlink written 6.4 years ago by Rob3.7k

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

ADD REPLYlink written 6.4 years ago by Botond Sipos1.7k
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