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Parameter Name | Variable | Default Value | Parameter Range | Description |
|---|---|---|---|---|
FRAG_UR_D0 | 1 | >0 | minimum length of fragments produced by hydrolysis | |
FRAG_UR_DELTA | NaN1 | geometry of the fragmentation process (1=linear, 2=surface-diameter, 3=volume-diameter, etc.); if not explicitly specified (NaN), the geometry of breakage depends logarithmically on the molecule length | ||
FRAG_UR_ETA | NaN1 | intensity of fragmentation, determining the number of breaks per unit length; if not explicitly specified (NaN), is determined by the corresponding corresponding value and an expectation of 200nt (or the mean filtered fragment size, if size selection is used) long fragments |
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The Flux Simulator uses a 3-step algorithm to tokenize a molecule; first, geometry and the number of fragments that are obtained from the molecule are determined. We found empirically that parameter d depends logarithmically on on , the length of the molecule that is fragmented . The number of fragments produced from a specific RNA molecule is determined by , where is the expectancy of the most abundant fragment size, computed from h and the gamma-function of :
Second, breakpoints are sampled uniformly from the interval [0;1[, resulting in relative length fractions for all all fragments. Third, relative fragment sizes are transformed from unit space to sizes that follow a Weibull distribution of shape d shape by:
where is a constant of the transformation to ensure that the sizes of the fragments sum up exactly to the given molecule length. Latter transformation produces a slightly distorted Weibull distribution for the sizes , however the deviation is sufficiently small to be neglected in our applications.
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