[mira_talk] est assembly strategy

Hi:
I've done some tests with mira and miraSearchESTSNPs, and I think that I'll 
have to use a more complex strategy than just using mira.
I have several sets of ESTs from different strains. Some of these strains are 
in fact samples created with mRNA from different individuals. This is a 
common approach when the objective is to look for SNPs because is cheaper to 
sequence all the strains in the same pool.

So my samples are a clear departure of the mira assumption than an unigene 
should have just one sequence. I'm aware of the problems introduced by a 
clustering step (where to draw the line to stop merging similar contigs?). 
But I can't use the mira output because mira is splitting the unigenes with 
SNPs in different contigs and in that way removing the possibility of finding 
SNPs in those contigs.
I've tried to use miraSearchESTSNPs but I don't understand well the proccess. 
I have a sample dataset that creates two similar contigs and 
miraSearchESTSNPs is not able of merging them. In fact they end up in 
remain_d_info in the second step and they are not taken into account in the 
thrid step. I've read the documentation but I still do not understand this 
process.

To solve this problem I'm thinking on following the pipeline:
- run mira with my 454, solexa and sanger reads,
- run tgicl (cap3) on the contig consensus to merge the very similar contigs.
- run mira again but with the map to a reference genome option set, using the 
result from tgicl as reference.
Do you think that this could work? Is there another simpler way?
Best regards,

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)

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