[mira_talk] Re: EST assembly from polyploids
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 22 Apr 2009 23:13:27 +0200
On Wednesday 22 April 2009 Schafleitner, Roland (CIP) wrote:
> [...]
> Would you have an idea how to modify the switches in order to mitigate
> the effect of many SNPs in large EST clusters without lowering the
> resolution of contig assembly from less abundant ESTs?
Hello Roland,
I'm not sure whether I understood you correctly: you want MIRA to be more
lenient in assembling some sequences but not in others? I'm just thinking loud
here: are you thinking of clustering?
If that's the case: MIRA itself was not built for clustering, but to really
find differences in your sequences. And therefore it dissociates the sequences.
But perhaps miraEST (now renamed miraSearchESTSNPs) might help you there. It's
a three step assembly, the last one configured to be more "clustering-like".
Did you have a look at it?
Regards,
Bastien
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