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  • 4.1.2 - Transcript Modifications

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Parameters

Name

Default

Value

Parameter

Range

Description
TSS_MEAN
25>0rate 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>0scale 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>0shape 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

Section

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).

Section
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).
Section

Output: One line per simulated transcript molecule containing in the LIB_FILE.