[mira_talk] Re: IUPc bases
- From: Adnan Niazi <niazi84@xxxxxxxxxxx>
- To: mira talk <mira_talk@xxxxxxxxxxxxx>
- Date: Sat, 12 Jun 2010 21:39:33 +0000
> If the qualities of two base groups are clear enough (say 60 for "A" but 20
> for "T"), MIRA will call a base. If they're not clear enough (say 23 for "A"
> and 26 for "T") it will be an IUPAC base.
and what if the coverage of low quality base in the column is higher than the
coverage of high quality base?
for example:
Consensus: TTTAAATT?CTA
TTTAAATTGCTA
TTTAAATTACTA
TTTAAATTaCTA
TTTAAATTaCTA
Reference read: TTTAAATTACTA
and how can we see the quality values of assembled paired end 75bp reads
obtained from illumina? so we can edit it manually. Is it possible in GAP4 and
any specific information file is required for it as there is no other file in
case of Illumina except reads.
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