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Parameter
| 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) |
Output
| Code Block |
|---|
[INFO] I am collecting information on the run.
initializing profiler **********
[INFO] Checking GTF file
********** OK (00:00:04)
[PROFILING] I am assigning the expression profile
********** OK (00:00:05)
Reading reference annotation ********** OK (00:00:08)
found 34102 transcripts
[PROFILING] Parameters
NB_MOLECULES 5000000
EXPRESSION_K -0.6
EXPRESSION_X0 5.0E7
EXPRESSION_X1 9500.0
PRO_FILE_NAME /Users/micha/Desktop/hg19_stranded.pro
profiling ********** OK (00:00:00)
Updating .pro file ********** OK (00:00:00)
molecules 4999517
[LIBRARY] creating the cDNA libary
Initializing Fragmentation File ********** OK (00:00:07)
4999517 mol initialized
[LIBRARY] Fragmentation UR
[LIBRARY] Configuration
D0: 1.0
Delta: Not specified, depends on sequence length
Eta: 350.0
Processing Fragments ********** OK (00:01:32)
47836171 mol: in 4999517, new 42836654, out 47836171
avg Len 315.81723, maxLen 996
preparing transcript sequences ********** OK (00:01:34)
[INFO] Initializing PWM cache
[INFO] Done
[LIBRARY] Reverse Transcription
[LIBRARY] Configuration
Mode: RH
PWM: default
RT MIN: 500
RT MAX: 5500
Processing Fragments ********** OK (00:10:16)
47890332 mol: in 47836171, new 54161, out 47890332
avg Len 181.1249, maxLen 1148
start amplification
[INFO] Loading default PCR distribution
[INFO] Initializing PWM cache
[INFO] Done
[LIBRARY] Amplification
[LIBRARY] Configuration
Rounds: 15
PCR Probability: 0.05
Processing Fragments ********** OK (00:02:21)
Amplification done.
In: 47890332 Out: 1291507850
47890332 mol: in 47890332, new 0, out 1291507850
avg Len 181.17375, maxLen 1127
Copied results to /Users/micha/Desktop/hg19_stranded.lib
Updating .pro file ********** OK (00:00:00)
[SEQUENCING] getting the reads
Initializing Fragment Index
Indexing ********** OK (00:00:41)
25701416 lines indexed (1291507850 fragments, 18682 entries)
sequencing ********** OK (00:43:11)
1291507850 fragments found (25701416 without PCR duplicates)
150003190 reads sequenced
8101165 reads fall in poly-A tail
54585326 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 3740 sec. |
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