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 | p | 0.7 | 0< p\leq 1 | 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 |
The efficiency of the polymerase chain reaction (PCR) amplification is either specified by an universal success rate p, or, by a normal distribution p= f(mean_{GC},SD_{GC}) 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:
P_S(N)= \sum_{0}^{\lceil \frac{N}{2} \rceil}P_{S-1}(N-k) {N-k \choose k} p^k (1-p)^{n-2k} |
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
\begin{array}{l} P_0=0 \\ P_1=\left\{ \begin{array}{rl} 1 &\mbox{ if $N=1$} \\ 0 &\mbox{ otherwise} \end{array} \right. \end{array} |