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Old 11-28-2011, 11:42 AM   #1
ians
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Location: St. Louis, MO

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Default pair_num_contigs in SOAPdenovo assembly

All,
I'm running SOAPdenovo 1.05 and it seems to be ignoring when i set the pair_num_contigs parameter in the cfg file. I try setting this to 1 for my library and it shows up as 1 in .peGrads (0 for the others). However, during the scaffolding step, the log reports that it is running with the parameter set to 5 (the default for LIMP).

Has anyone gotten this parameter to work? Others have tried lowering and raising this parameter with little success: http://groups.google.com/group/bgi-s...dab51ac4?pli=1
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