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Parameter
| Name | Variable | Default Value | Parameter Range | Description |
|---|---|---|---|---|
REF_FILE | file from which the reference annotation (GTF format) is read | |||
LOAD_CODING | true | {true,false} | flag to dis-/consider transcripts that have an annotated coding sequence | |
LOAD_NONCODING | true | {true,false} | flag to dis-/consider transcripts that are annotated to be non-coding | |
PRO_FILE | file to which the simulated expression values are written | |||
LIB_FILE | file to which the expressed transcript molecules are written | |||
NB_MOLECULES | 5,000,000 | >0 | number of expressed RNA molecules simulated | |
EXPRESSION_K | -0.6 | exponent of the expression power law ("Pareto coefficient") | ||
EXPRESSION_X0 | 9,500 | controls the exponential decay | ||
EXPRESSION_X1 | 9,5002 | controls the exponential decay |
The Distribution of Gene Expression Levels
| Section |
|---|
In the beginning, the Flux Simulator reads the transcripts of the reference annotation and clusters genomic overlapping ones into loci. To assign The cell group of the experiment is assigned a random expression profile where not necessarily all transcripts of the reference are expressed. Expression levels y are levels are connected with the relative expression rank x by a mixed power exponential power- and exponential law of the general form |
| Section |
|---|
where denotes the rank number of a gene, the expression level of the highest abundant gene , and is the exponent of the underlying intrinsic power law, and respectively control the exponential decay. The Flux Simulator assigns to the transcripts in the reference annotation randomly expression ranks .Subsequently, these ranks which then are turned into numbers of virtual molecules relative expression levels by the modified Zipf's Law above. Usually, part of the transcripts from the reference annotation will remains unexpressed., which determines the initial number of molecules by multiplication with the total numbers of molecules. Default values for parameters and have been estimated for mammalian cells by non-linear fitting to expression levels observed in experimental results. |
| Section |
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Output: The first 6 columns of the PRO_FILE |
Transcript Modifications during Expression
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