[mira_talk] Re: CT tag acronyms in .ace files

Thanks heaps Bastien, that is a great start, we will try it asap! 

We have a student here now looking into the detection of homopolymer errors; we 
will keep the list updated on what his findings are, and if there is anything 
that can help improving the assembly.

Regards
Björn



On Tue, 28 Jul 2009 23:27:31 +0200
Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

> On Samstag 25 Juli 2009 Björn Nystedt wrote:
> > one thing that would be very nice to tag would be potential frameshifts in
> > 454 data due to homopolymer errors. This would be a tag at sites where
> > about half of the 454 reads call (the same) base and the rest call a gap
> > (the cutoffs here could be discussed). In principle, these sites could have
> > turned up in the SNP tag 'SAOc', but I don't think it does?
> 
> Hello Björn,
> 
> the S?Oc tags are reserved for SNPs between strains. But I've added a new tag 
> "DGPc": Dubious Gap Position on Consensus which is set whenever the number of 
> gaps is 40-60% (I didn't have time tonight to make that configurable) of the 
> number of bases from the next frequent base.
> 
> Try version 3rc1a (which I've just uploaded) and tell me whether this suits 
> your needs.
> 
> > In a hybrid assembly, this would also be sites where the basecalls from
> > non-454 reads would be preferred in the consensus, even when 454 data
> > dominate in coverage, so it could be used to automatically improve the
> > consensus quality during the assembly, if this is not allready taken into
> > account somehow?
> 
> It is taken into account in hybrid assemblies already. Those site are tagged 
> STMS or STMU depending on whether MIRA thinks it could correctly resolve the 
> problem or not (although STMS and STMU are also set for differences not 
> involving gaps).
> 
> Regards,
>   Bastien
> 
> 
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-- 
====================================
Björn Nystedt
PhD Student
Molecular Evolution
EBC, Uppsala University
Norbyv. 18C, 752 36  Uppsala
Sweden
phone: +46 (0)18-471 45 88
email: Bjorn.Nystedt@xxxxxxxxx
====================================

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