[mira_talk] quantity vs quality of SNP predictions

Hi all,

Following Bastien's advises i've seen in this list previously, 
i have used very strict parameters to assemble 454 data in order to detect 
potential SNPs with a good confidence.

Problem is, using these parameters, the number of reads falling into 
debrislist reaches 60%,
and out of the 40% remaining reads used during assembly only 25% en up in 
contigs with
good enough coverage for SNP detection.

At the end, only 10% of the reads were effectively used to predict 
potential SNP positions...

Does someone else have similar results ? Or is it that my reads are really 
of low quality ?

Is it really worth it to loose 90% of reads in order to gain in confidence 
of SNPs discovered ?

Did someone tried using different parameter settings in order to evaluate 
sensitivity vs specificity of SNP detection with mira ?

The species i'm working with is a polyploid eukaryote, and the sequences 
are PCR amplicons which were ligated before sonication
and 454 titanium sequencing on 4 different cultivars.

I've developped a script in order to detect and split potential chimeras, 
and although it worked quite well,
i'm pretty sure i didn't detect all chimeric sequences. So if someone 
knows of a tool which does this kind of clipping, 
i'd also like to hear from him !!!

Thanks for any comments or feelings you could have on these topics,

jorge.
--- 
Jorge Duarte
Bioinformatics Research Engineer
BIOGEMMA - Upstream Genomics Group
Z.I. Du Brézet
8, Rue des Frères Lumière
63028 CLERMONT FERRAND Cedex 2
FRANCE
Tel : +33 (0)4 73 39 60 73
Fax : +33 (0)4 73 39 60 71
E-mail : jorge.duarte@xxxxxxxxxxxx

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