Details
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Bug
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Status: Resolved
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Major
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Resolution: Won't Fix
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Simulator 1.0.3 (API 1.12)
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None
Description
LOAD_CODING true LOAD_NONCODING true NB_MOLECULES 8000000 EXPRESSION_K -0.6 EXPRESSION_X0 9500.0 EXPRESSION_X1 9.025E7 TSS_MEAN NaN POLYA_SCALE NaN POLYA_SHAPE NaN RTRANSCRIPTION true RT_LOSSLESS true RT_MAX 5500 RT_MIN 50 RT_PRIMER RH FRAGMENTATION true FRAG_SUBSTRATE RNA FRAG_METHOD UR FRAG_UR_D0 1 FRAG_UR_DELTA NaN FILTERING true PCR_DISTRIBUTION default PAIRED_END true READ_LENGTH 76 ERR_FILE 76 READ_NUMBER 15000000 FASTA true
When I use the parameter file listed at the very beginning, that is, no SIZE_DISTRIBUTION, TSS_MEAN, POLYA_SCALE, POLYA_SHAPE and it runs successfully, The UR fragmentation results in average fragment length of 188 with maximum of 555 and a total of 76 million molecules. And when doing a size selection on this, the output average is 181 with max: 299 and gives me 2.1 million molecules which is approximately 3% of total molecules from fragmentation. How is this possible? The average is 188 out of 76 million and you get at the end 2 million between 181 and 299…?? It just doesn't add up, does it? Or did I get it completely wrong?
[LIBRARY] Configuration
Mode: RH
PWM: No
RT MIN: 50
RT MAX: 5500
Processing Fragments ********** OK (00:05:34)
76054743 mol: in 76027642, new 27101, out 76054743
avg Len 156.77885, maxLen 555
initializing Selected Size distribution
[LIBRARY] Segregating cDNA (Acceptance)
Processing Fragments ********** OK (00:02:05)
76054743 mol: in 76054743, new 0, out 2057527
avg Len 181.46268, maxLen 299
start amplification