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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
POLYA_SCALE
300>0scale parameter of the Weibull distribution describing poly-A tail lengths
POLYA_SHAPE
2>0shape paramter of the Weibull distribution describing poly-A tail lengths

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).

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