newbler, parameters to improve my cDNA assembly de novo

[AleixArnau]

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!

[flxlex]

Closed due to double posting (bioinformatics forum)