Parameters
Name | Default Value | Parameter Range | Description |
|---|---|---|---|
TSS_MEAN | 25 | >0 | rate of the exponential for deviation of simulated transcription starts from annotated transcription start point, set to NaN (i.e., "not a number") to deactivate simulated transcription start variability |
POLYA_SCALE | 300 | >0 | scale parameter of the Weibull distribution describing poly-A tail lengths, set to NaN (i.e., "not a number") to deactivate simulated poly-A tails |
POLYA_SHAPE | 2 | >0 | shape paramter of the Weibull distribution describing poly-A tail lengths, set to NaN (i.e., "not a number") to deactivate simulated poly-A tails |
Algorithm
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).
Based on the number of RNA copies 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).
Output: One line per simulated transcript molecule containing in the LIB_FILE.
Overview
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