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Old 09-06-2012, 07:38 AM   #1
Junior Member
Location: Buenos Aires

Join Date: Sep 2012
Posts: 1
Default 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

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