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Parameter

Variable

Parameter

Name

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
The Distribution of Gene Expression Levels
 
Parameter
Name
Variable
Default
Value
Parameter
Range
Description
NB_MOLECULES
 5,000,000>0number of expressed RNA molecules simulated
EXPRESSION_K
-0.6exponent of the expression power law ("Pareto coefficient")
EXPRESSION_X0
9,500parameter of the exponential decay
EXPRESSION_X1
9,5002parameter of the exponential decay
TSS_MEAN    
POLYA_SCALE    
POLYA_SHAPE   
The Distribution of Gene Expression Levels
 Section
Input: reference annotation (REF_FILE), transcript filtering parameter (LOAD_CODING, LOAD_NONCODING), expression parameters (NB_MOLECULES, EXPRESSION_K, EXPRESSION_X0, EXPRESSION_X1)
...
Transcript Modifications during Expression
Parameter
Name
Default
Value
Parameter
Range
Description
TSS_MEAN
25>0rate of the exponential for deviation of simulated transcription starts from annotated transcription start point
POLYA_SCALE
300>0scale parameter of the Weibull distribution describing poly-A tail lengths
POLYA_SHAPE
2>0shape paramter of the Weibull distribution describing poly-A tail lengths
 Section
Input: Columnn 6 of the PRO_FILE, i.e., the absolute number of RNA molecules that is simulated for a certain transcript in the experiment and the parameters of transcription start (TSS_MEAN) and poly-A tail variation (POLYA_SCALE, POLYA_SHAPE).
 Section
After for each transcript Based on the number of RNA copies has been determined, these in silico expressed transcripts are that is simulated for each transcript, genes are in silico expressed. In this process,  assigned individual variations in transcription start and the length of the attached poly-A tail. The Flux Simulator models differences in the annotated transcription starts by an exponential distribution with an adjustable mean value (TSS_MEAN). During poly-adenylation in the nucleus usually 200-250 adenine residues get added to the primary transcript. Disregarding other poly-adenylation mechanisms (e.g., cytoplasmatic polyadenylation) the Flux Simulator describes poly-A lengths by a flexible Weibull distribution (POLYA_SCALE, POLYA_SHAPE).
...