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_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_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 | YES | Paired-end reads are simulated, two per fragment |
[INFO] Checking GTF file ********** OK (00:00:04) [PROFILING] I am assigning the expression profile ********** OK (00:00:05) Reading reference annotation ********** OK (00:00:07) 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 [LIBRARY] creating the cDNA libary Initializing Fragmentation File ********** OK (00:00:05) 4999457 mol initialized [LIBRARY] Fragmentation UR [LIBRARY] Configuration D0: 1.0 Delta: Not specified, depends on sequence length Eta: 170.0 Processing Fragments ********** OK (00:02:34) 93363234 mol: in 4999457, new 88363777, out 93363234 avg Len 154.08191, maxLen 513 preparing transcript sequences ********** OK (00:01:21) [LIBRARY] Reverse Transcription [LIBRARY] Configuration Mode: RH PWM: No RT MIN: 500 RT MAX: 5500 Processing Fragments ********** OK (00:05:32) 93363234 mol: in 93363234, new 0, out 93347200 avg Len 145.28108, maxLen 506 initializing Selected Size distribution [LIBRARY] Segregating cDNA (MCMC Filter) Processing Fragments ********** OK (00:03:14) 93347200 mol: in 93347200, new 0, out 49712978 avg Len 153.1023, maxLen 299 start amplification [INFO] Loading default PCR distribution [LIBRARY] Amplification [LIBRARY] Configuration Rounds: 15 Mean: 0.5 Standard Deviation: 0.1 Processing Fragments ********** OK (00:03:13) Amplification done. In: 49712978 Out: 1340698400 49712978 mol: in 49712978, new 0, out 1340698400 avg Len 153.10666, 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 (00:00:30) 26681880 lines indexed (1340698400 fragments, 18750 entries) sequencing ********** OK (00:35:05) 1340698400 fragments found (26681880 without PCR duplicates) 29993750 reads sequenced 2314644 reads fall in poly-A tail 2538184 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 3252 sec.