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| Expression | ||
| NB_MOLECULES | 5,000,000 | Number of RNA molecules initially in the experiment |
| TSS_MEAN | 25 | Average deviation from the annotated transcription start site (TSS) |
| POLYA_SCALE | 80 | Scale of the Weibull distribution, shifts the average length of poly-A tail sizes |
| POLYA_SHAPE | 2 | Shape of the Weibull distribution describing poly-A tail sizes |
| Reverse Transcription | ||
| RTRANSCRIPTION | YES | Switch on the reverse transcription |
| RT_PRIMER | PDT | Use poly-dT primers used for first strand synthesis |
| 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 | 2,500 | Maximum length observed after reverse transcription of full-length transcripts |
| Fragmentation | ||
| FRAG_SUBSTRATE | DNA | Specifies DNA as the substrate of fragmentation, either DNA or RNA |
| FRAG_METHOD | EZ | Enzymatic digestion as fragmentation method |
| FRAG_EZ_MOTIF | DNAseI.pwm | Fragmentation by enzymatic digestion |
| Amplification and Size Segregation | ||
| PCR_DISTRIBUTION | default | Default PCR distribution with 15 rounds and 20 bins |
| GC_MEAN | 0.5 | Mean value of a gaussian distribution that reflects GC bias amplification probability |
| GC_SD | 0.1 | Standard deviation of a gaussian distribution that reflects GC bias amplification probability |
| FILTERING | YES | Enables size filtering of fragments |
| SIZE_SAMPLING | MH | The Metropolis-Hastings algorithm is used for filtering |
| Sequencing | ||
| READ_NUMBER | 1,000,000 | Produce 1 million reads |
| READ_LENGTH | 36 | Each read sequence is 36nt long |
| PAIRED_END | NO | Single reads are simulated, one per fragment |
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