Parameters
Parameter Name | Variable | Default Value | Parameter Range | Description |
|---|---|---|---|---|
FRAGMENTATION | ||||
FRAG_METHOD | ||||
FRAG_SUBSTRATE |
Overview
Next, an optional fragmentation process (nebulization, hydrolysis, adaptive focusing acoustics, …) may be comprised in the simulation. In general the simulation distinguishes 2 different mechanisms of RNA degradation, a mechanical/physical breaking process (PHYSICAL) and cleavage that is less dependant on physical properties (CHEMICAL). Choice of the fragmentation nature will influence the distribution of fragment lengths after the simulated fragmentation. Furthermore, also dependant on the adopted method, you should provide a realistic estimation of the maximum molecule length (FRAG_LAMBDA) that is not broken in the applied protocol. For instance, ~500nt cDNA molecules are known to be problematic to break with usual nebulization strategies. Naturally, this will mark about the upper limit of the fragment distribution yielded.
Overview
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