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Old 03-25-2014, 06:49 AM   #1
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Location: Barcelona

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Default newbler, parameters to improve my cDNA assembly de novo

I'm trying to assemble de novo cDNA reads from transcriptome of Begonia using Newbler but actually the result isn't really good... I've used the configured parameters since it's my first assembly. I would like to know, if there are someone who used to run Newbler, which parameters could I change in order to improve my results. That are the parameters:

Input: minimum read length: 20 Computation: seed step:12 seed length:16 seed count:1 minimum overlap length:40 minimun overlap identity:90 alignment identity score: 2 alignment difference score:-3

Thanks for all!
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Old 03-26-2014, 02:29 AM   #2
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Closed due to double posting (bioinformatics forum)
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