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) |
Code Block |
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[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. |