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Parameter Name | Default Value | Parameter Range | Description |
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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 |
The Distribution of Gene Expression Levels
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Parameter
Name
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Default
Value
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Parameter
Range
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NB_MOLECULES
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EXPRESSION_K...
EXPRESSION_X0...
EXPRESSION_X1...
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Input: reference annotation (REF_FILE), transcript filtering parameter (LOAD_CODING, LOAD_NONCODING), expression parameters (NB_MOLECULES, EXPRESSION_K, EXPRESSION_X0, EXPRESSION_X1) |
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where denotes the rank number of a gene and is the exponent of the intrinsic power law, and respectively control the exponential decay. The Flux Simulator assigns to the transcripts in the reference annotation randomly expression ranks which then are turned into relative expression levels by the modified Zipf's Law above, 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. |
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Transcript Modifications during Expression
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Overview
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