Name |
Default Value |
Parameter Range |
Description |
---|---|---|---|

TSS_MEAN |
25 | >0 | rate of the exponential for deviation of simulat= ed transcription starts from annotated transcription start point, set to Na= N (i.e., "not a number") to deactivate simulated transcription start variab= ility |

POLYA_SCALE |
300 | >0 | scale parameter of the Weibull distribution desc= ribing 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 descr= ibing poly-A tail lengths, set to NaN (i.e., "not a number") to deactivate = simulated poly-A tails |

**Input**: Columnn 6 of the PRO_FILE, i.e., the absolute nu=
mber of RNA molecules that is simulated for a certain transcript in the exp=
eriment and the parameters of transcription start (TSS_MEAN) and poly-A tai=
l variation (POLYA_SCALE, POLYA_SHAPE).

Based on the number of RNA copies that is simulated for each transcript, ge=
nes are=20
*in silico* expressed. In this process, assigned individual va=
riations in transcription start and the length of the attached poly-A tail.=
The Flux Simulator models differences in the annotated transcription start=
s 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 mecha=
nisms (e.g., cytoplasmatic polyadenylation) the Flux Simulator describes po=
ly-A lengths by a flexible Weibull distribution (POLYA_SCALE, POLYA_SHAPE).

**Output**: One line per simulated transcript molecule cont=
aining in the LIB_FILE.