[mira_talk] Re: How does Mira determine quality scores?

On Mittwoch 29 Juli 2009 Davide Sassera wrote:
> I found that often in situations of long homopolymers the presence of
> few reads containing "1 more base" overcomes the presence of many more
> reads with "1 less base" in the consensus.

Hello Davide,

I need to take back some of my statements. While working on TCS output today, 
I re-checked the consensus computation for 454. It actually is not what I 
thought it would be, but even simpler: in 454 sequences, majority wins. So, 
ich you have 30 gaps and two reads with a base, you should always have a gap.

Question is, where did you see the case where a lot of gaps were overturned by 
a few bases? Would you have an example for that and also specify where you saw 
it (in MIRA result files, in a finishing program) etc.pp.

Regards,
  Bastien


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