Page History
...
| Key | Type | Default Value | Description |
|---|---|---|---|
| LOAD_CODING | Boolean | YES | Coding messengers, i.e., transcripts that have an annotated CDS, are extracted from the cell. |
| LOAD_NONCODING | Boolean | YES | Non-coding RNAs, i.e., transcripts without an annotated ORF are extracted from the cell. |
| NB_MOLECULES | Long | 5,000,000 | Number of RNA molecules initially in the experiment. |
| EXPRESSION_K | Double | (-0.6) | Exponent of power-law underlying the expression profile [-1;0] |
| EXPRESSION_X0 | Double | 9,500 | Linear parameter of the exponential decay. |
| EXPRESSION_X1 | Double | 90,250,000 | Quadratic parameter of the exponential decay. |
Transcript Modifications
| Key | Type | Default Value | Description |
|---|---|---|---|
TSS_MEAN | Double | 25 | 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 | Double | 300 | 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 | Double | 2 | 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 |
Library prepeparation
Fragmentation
| Key | Type | Default Value | Description |
|---|---|---|---|
| FRAGMENTATION | Boolean | YES | Turn fragmentation on/off. |
| FRAG_SUBSTRATE | {DNA,RNA} | RNA* *DNA in Simulator v1.2 and earlier | Substrate of fragmentation, determines the order of fragmentation and reverse transcription (RT): for substrate DNA, fragmentation is carried out after RT, substrate RNA triggers fragmentation before RT. |
| FRAG_METHOD | {EZ,NB,UR} | UR | Fragmentation method employed: * [EZ] Fragmentation by enzymatic digestion * [NB] Fragmentation by nebulization * [UR] Uniformal random fragmentation |
Enzymatic Digestion | |||
| FRAG_EZ_MOTIF | String | Sequence motif caused by selective restriction with an enzyme, choose pre-defined NlaIII, DpnII, or a file with a custom position weight matrix. | |
| Nebulization | |||
| FRAG_NB_LAMBDA | Double | 900.0 | Threshold on molecule length that cannot be broken by the shearfield of nebulization. |
| FRAG_NB_THOLD | Double | 0.1 | Threshold on the fraction of the molecule population; if less molecules break per time unit, convergence to steady state is assumed. |
| FRAG_NB_M | Double | 1.0 | Strength of the nebulization shearfield (i.e., rotor speed). |
| Uniformal Random (UR) Fragmentation | |||
| FRAG_UR_ETA | Double | NaN | Average expected framgent size after fragmentations, i.e., number of breaks per unit length (exhautiveness of fragmentation); NaN optimizes the fragmentation process w.r.t. the size filtering |
| FRAG_UR_DELTA | Double | NaN | Geometry of molecules in the UR process: * NaN= depends logarithmically on molecule length, * 1= always linear, * 2= always surface-diameter, * 3= volume-diameter, ... |
| FRAG_UR_D0 | Double | 1.0 | Minimum length of fragments produced by UR fragmentation. |
...
Overview
Content Tools