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Parameter
Parameter Name | Variable | Default Value | Parameter Range | Description |
|---|---|---|---|---|
PCR_DISTRIBUTION | default | {default, none, file} | parameter specifies the name of a PCR distribution file, or 'default' to use a distribution with 15 rounds and 20 bins. A value of 'none' disables PCR amplification. | |
PCR_PROBABILITY | 0.7 | duplication probability in each step of the simulated PCR. The parameter value is only taken into account if GC_MEAN is 'NaN'. | ||
GC_MEAN | meanGC | 0.5 | NaN, 0 < meanGC < 1 | mean of duplication probability distribuiton with respect to GC content; the distribution is approximated by a normal distribution. A value of 'NaN' disables the GC-dependency of PCR and employs the (constant) probability PCR_PROBABILITY |
GC_SD | SDGC | 0.1 | 0 < SDGC < 1 | standard deviation of duplication probability distribuiton with respect to GC content |
Algorithm
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The efficiency of the polymerase chain reaction (PCR) amplification is either specified by an universal success rate rate , or, by a normal distribution parameterized to capture GC preferential biases (defaultmeanGC=0.5 and SDGC=0.1). Given p, the number of copies produced from a certain fragment is determined by random sampling under the cumulative binomial:
with S denoting the PCR cycle and N the number of molecules. As default, we assume 15 PCR cycles (S=15), and sample randomly the number of duplicates yielded by PCR amplification under the corresponding probability distribution P15(N) for all possible values of N=[1;215]. The recursion terminates by
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