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Parameter
| 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 | 300 | 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 |
| Fragmentation | ||
| FRAG_SUBSTRATE | RNA | Specifies RNA as the substrate of fragmentation |
| FRAG_METHOD | UR | Uniform random fragmentation |
| FRAG_UR_ETA | 170 | 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 | 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_DISTRIBUTION | null | Employ an empirical Illumina fragment size distribution |
| SIZE_SAMPLING | MH | The Metropolis-Hastings algorithm is used for filtering |
| Sequencing | ||
| READ_NUMBER | 15,000,000 | Produce 15 million reads |
| READ_LENGTH | 75 | Each read sequence is 75nt long |
| PAIRED_END | ||
...
| NO | Single reads are simulated (one per fragment) |
Output
...
| Code Block |
|---|
[INFO] I am collecting information on the run. initializing profiler ********** [INFO] Checking GTF file ********** OK (00:00:04 03) [PROFILING] I am assigning the expression profile ********** OK (00:00:05) Reading reference annotation ********** OK (00:00:07 06) found 28045 transcripts
[PROFILING] Parameters
NB_MOLECULES 5000000
EXPRESSION_K -0.6
EXPRESSION_X0 5.0E7
EXPRESSION_X1 9500.0
PRO_FILE_NAME /Users/micha/Desktop/mm9_hydrolysis.pro
profiling ********** OK (00:00:00)
Updating .pro file ********** OK (00:00:00)
molecules 4999457
4999480 [LIBRARY] creating the cDNA libary Initializing Fragmentation File ********** OK (00:00:05 06)4999457 4999480 mol initialized [LIBRARY] Fragmentation UR [LIBRARY] Configuration D0: 1.0 Delta: Not specified, depends on sequence length Eta: 170.0
Processing Fragments ********** OK (00:0203:34 20)93363234 99433550 mol: in4999457 4999480, new88363777 94434070, out93363234 99433550 avg Len 154.08191 13617, maxLen513 499 preparing transcript sequences ********** OK (00:01 02:21 04) [INFO] Initializing PWM cache [INFO] Done [LIBRARY] Reverse Transcription [LIBRARY] Configuration Mode: RH PWM:No motif_1mer_0-5.pwm RT MIN: 500 RT MAX: 5500
Processing Fragments ********** OK (00:0518:32 53)93363234 99436361 mol: in93363234 99433550, new0 2811, out93347200 99436361 avg Len145 226.28108 49129, maxLen506 718 initializing Selected Size distribution [LIBRARY] Segregating cDNA (MCMC Filter Acceptance) Processing Fragments ********** OK (00:03 02:14 32)93347200 99436361 mol: in93347200 99436361, new 0, out49712978 3935454 avg Len153 183.1023 18074, maxLen 299 start amplification [INFO] Loading default PCR distribution [INFO] Initializing PWM cache [INFO] Done [LIBRARY] Amplification [LIBRARY] Configuration Rounds: 15 Mean: 0.5 Standard Deviation: 0.1
Processing Fragments ********** OK (00:0300:13 19) Amplification done. In:49712978 3935454 Out:1340698400 10611152549712978 3935454 mol: in49712978 3935454, new 0, out1340698400 106111525 avg Len153 183.10666 16734, maxLen 299 Copied results to /Users/micha/Desktop/mm9_hydrolysis.lib Updating .pro file ********** OK (00:00:00)
[SEQUENCING] getting the reads
Initializing Fragment Index
Indexing ********** OK (00:00:3003)26681880 2112053 lines indexed (1340698400 106111525 fragments,18750 16421 entries) sequencing ********** OK (00:35 04:05 11)
1340698400106111525 fragments found (26681880 2112053 without PCR duplicates)29993750 15000653 reads sequenced2314644 2333333 reads fall in poly-A tail2538184 511978 truncated reads
Moving temporary BED file
Updating .pro file ********** OK (00:00:00)
Updating .pro file ********** OK (00:00:00)
Updating .pro file ********** OK (00:00:00)
Updating .pro file ********** OK (00:00:00)
[END] I finished, took me 32522291 sec. |
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