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  • MetaSim: why paired end reverse read is much shorter than forward read??

    Hi everyone! I'm new here...

    I simulated a library paired end 20 kb for 454 technology using MetaSim... but always the reverse read is so much shorter than forward read (forward average: 300 pb and reverse average: 50 pb)

    Somebody have any idea why???

    I checked the preset of the program and it looks right... so, I don't get it!

    Preset Name: 454
    Number Of Reads / Mate Pairs=100000
    Error Model=454

    454 Error Model Configuration=
    Number Of Cycles: 137 (~349 Base Pairs)
    Mate Pair Probability: 0.99
    Mate Pair Read Length: 350
    Remove Mate Pair Linker from Output: true
    Lognormal Distribution Mean: 0.23
    Lognormal Distribution Std. Deviation: 0.15
    Proportionality Constant for Std. Deviation: 0.15
    Scale Std. Deviation with Square Root of Mean: true
    Generate Signal Trace: false

    454 Error Model DNA Clone Parameters=
    Distribution: Normal
    Mean: 20000.0
    2nd parameter: 3000.0

    Combine All Files=false
    Uniform Sequence Weights=false
    Number Of Threads=4
    Write FastA=true
    Compress Output Files=false

    regards!!

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