[mira_talk] Re: consensus sequence & alignment gap

On 06/29/2012 10:57 PM, Markiyan Samborskyy wrote:

1. Did you switch on the automatic consensus editor (ace=1) for 454 or
iontorrent? - If it is on those errors shouldn't happen.


He most probably had: it's default for MIRA to have it on.


3. [...] Was the input reads
technology set to Iontorrent or 454?


Yes, it was, the QV of "1" for his gaps was a give-away.


4. Did the quality got loaded OK? Was the homopolymer quality vallues
reprocessed (so the the first and the last bases in the homopolymer
are lover by a factor of 10, then the middle ones?
Hmmm ... there's the beginning of an idea. I quickly looked up what you did in sff2phd and I'm not quite sure I liked the approach of forcing quality values down. But this gave me the idea of redistributing those values and that actually might work painlessly. I'll make a couple of experiments. 

B.


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