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Reference Annotation

Parameter File

Reference Genome

Parameter

Expression
NB_MOLECULES5,000,000Number of RNA molecules initially in the experiment
TSS_MEAN50Average deviation from the annotated transcription start site (TSS)
POLYA_SCALENaNScale of the Weibull distribution, shifts the average length of poly-A tail sizes
POLYA_SHAPENaNShape of the Weibull distribution describing poly-A tail sizes
Fragmentation
FRAG_SUBSTRATERNASpecifies RNA as the substrate of fragmentation
FRAG_METHODURUniform random fragmentation
FRAG_UR_ETA350Average expected framgent size after fragmentations, i.e., number of breaks per unit length (exhautiveness of fragmentation)
FRAG_UR_D01Minimum length of fragments produced by UR fragmentation
FRAG_UR_DELTANaNGeometry of molecules in the UR process depends logarithmically on molecule length
Reverse Transcription
RTRANSCRIPTIONYESSwitch on the reverse transcription
RT_PRIMERRHUse random hexamer primers used for first strand synthesis
RT_MOTIFdefaultA default PWM of the current Illumina protocol is used
RT_LOSSLESSYESFlag to force every molecule to be reversely transcribed
RT_MIN500Minimum length observed after reverse transcription of full-length transcripts
RT_MAX5,500Maximum length observed after reverse transcription of full-length transcripts
Amplification and Size Segregation
PCR_DISTRIBUTIONdefaultDefault PCR distribution with 15 rounds and 20 bins
GC_MEANNaNDisable GC biases
PCR_PROBABILITY0.05PCR duplication probability
FILTERINGNODisable size selection
Sequencing
READ_NUMBER150,000,000Produce 15 million reads
READ_LENGTH75Each read sequence is 75nt long
PAIRED_ENDYESPaired-end reads are simulated (two per fragment)

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