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

Dear Bastien, 

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? 

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?

Best regards
Björn Nystedt




On Sat, 25 Jul 2009 16:47:09 +0200
Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

> On Freitag 24 Juli 2009 David Hesselbom wrote:
> > I'm trying to figure out how to interpret this tag found in a .ace file:
> >
> > CT{
> > m07aNrPeM07_lrc2716 H454 MIRA 2101 2101 020202:121212 NoTrans
> > No edit. PL: 3 RS: 6 RL: 1 RWTS: 0 EL: 1
> > }
> > The first rows are pretty straightforward, but what about the third one?
> > What are PL, RS, RL, RWTS and EL? I've looked everywhere I can think of for
> > an explanation of these acronyms without finding one. Since the tag is
> > created by Mira (or isn't it?), this seems like the right place to ask
> > about it. Is there a document somewhere that explains what the acronyms
> > are, and if so, can someone please tell me where to find this document?
> 
> Hello David,
> 
> they're created by MIRA but you don't want to figure out what the third line 
> means ... it's just some statistics from the 454 read editor put into the tag 
> for me to track in case of misedits. I think I could even start to remove 
> that 
> output as the editor got pretty good at not editing when it shouldn't :-)
> 
> 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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