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]

the result isn't really good...

You really need to specify what you mean by that. Also, giving a bit of information an what kind and how many reads you have will help too...

[AleixArnau]

It's the transcriptome of a specie of Begonia, about 250.000 reads sequenced by 454. We want to assembly again because in next steps did a BLAST of isotigs from each isogroup against the genome and that showed that ~50% of isogroups with >1 isotig matched different genome contigs, suggesting these were incorrectly assigned as alternative transcripts. So, we would like to know which parameters we can change to try to improve our assembly for that transcriptome.

Thanks!

[flxlex]

How big is the genome and expected transcriptome? how much coverage do you have? How good is the assembly? You mapping could be explained by the genome contigs being very fragmented, some of them having just one exon, for example...