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| Expression | ||
|---|---|---|
| NB_MOLECULES | 5,000,000 | Number of RNA molecules initially in the experiment |
| TSS_MEAN | 50 | Average deviation from the annotated transcription start site (TSS) |
| POLYA_SCALE | 100NaN | Scale of the Weibull distribution, shifts the average length of poly-A tail sizes |
| POLYA_SHAPE | 1.5NaN | Shape of the Weibull distribution describing poly-A tail sizes |
| Fragmentation | ||
| FRAG_SUBSTRATE | RNA | Specifies RNA as the substrate of fragmentation |
| FRAG_METHOD | UR | Uniform random fragmentation |
| FRAG_UR_ETA | 350 | Average expected framgent size after fragmentations, i.e., number of breaks per unit length (exhautiveness of fragmentation) |
| FRAG_UR_D0 | 1 | Minimum length of fragments produced by UR fragmentation |
| FRAG_UR_DELTA | NaN | Geometry of molecules in the UR process depends logarithmically on molecule length |
| Reverse Transcription | ||
| RTRANSCRIPTION | YES | Switch on the reverse transcription |
| RT_PRIMER | RH | Use random hexamer primers used for first strand synthesis |
| RT_MOTIF | default | A default PWM of the current Illumina protocol is used |
| RT_LOSSLESS | YES | Flag to force every molecule to be reversely transcribed |
| RT_MIN | 500 | Minimum length observed after reverse transcription of full-length transcripts |
| RT_MAX | 5,500 | Maximum length observed after reverse transcription of full-length transcripts |
| Amplification and Size Segregation | ||
| PCR_DISTRIBUTION | default | Default PCR distribution with 15 rounds and 20 bins |
| GC_MEAN | NaN | Disable GC biases |
| PCR_PROBABILITY | 0.05 | PCR duplication probability |
| FILTERING | NO | Disable size selection |
| Sequencing | ||
| READ_NUMBER | 150,000,000 | Produce 15 million reads |
| READ_LENGTH | 75 | Each read sequence is 75nt long |
| PAIRED_END | YES | Paired-end reads are simulated (two per fragment) |
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