Input
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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
[INFO] I am collecting information on the run.
initializing profiler **********
[INFO] Checking GTF file
********** OK (00:00:03)
[PROFILING] I am assigning the expression profile
********** OK (00:00:05)
Reading reference annotation ********** OK (00:00:06)
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 4999480
[LIBRARY] creating the cDNA libary
Initializing Fragmentation File ********** OK (00:00:06)
4999480 mol initialized
[LIBRARY] Fragmentation UR
[LIBRARY] Configuration
D0: 1.0
Delta: Not specified, depends on sequence length
Eta: 170.0
Processing Fragments ********** OK (00:03:20)
99433550 mol: in 4999480, new 94434070, out 99433550
avg Len 154.13617, maxLen 499
preparing transcript sequences ********** OK (00:02:04)
[INFO] Initializing PWM cache
[INFO] Done
[LIBRARY] Reverse Transcription
[LIBRARY] Configuration
Mode: RH
PWM: motif_1mer_0-5.pwm
RT MIN: 500
RT MAX: 5500
Processing Fragments ********** OK (00:18:53)
99436361 mol: in 99433550, new 2811, out 99436361
avg Len 226.49129, maxLen 718
initializing Selected Size distribution
[LIBRARY] Segregating cDNA (Acceptance)
Processing Fragments ********** OK (00:02:32)
99436361 mol: in 99436361, new 0, out 3935454
avg Len 183.18074, 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 (00:00:19)
Amplification done.
In: 3935454 Out: 106111525
3935454 mol: in 3935454, new 0, out 106111525
avg Len 183.16734, 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 (00:00:03)
2112053 lines indexed (106111525 fragments, 16421 entries)
sequencing ********** OK (00:04:11)
106111525 fragments found (2112053 without PCR duplicates)
15000653 reads sequenced
2333333 reads fall in poly-A tail
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 2291 sec.
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