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In the beginning, the Flux Simulator reads the transcripts of the reference annotation (REF_FILE) and clusters genomic overlapping ones into loci. Transcripts that are annotated as non-/coding can be selectively disregarded (LOAD_CODING, LOAD_NONCODING). Then to assign a random expression profile where not necessarily all transcripts of the reference are expressed. Expression levels
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y = y_0 x^{k} exp^{-\frac{x}{a}-\left(\frac{x}{b}\right)^2} |
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