[mira_talk] Re: Fwd: ace file output from MIRA

Hi,
generally RT tags do appear in the corresponding RD section for each read
separately, that is,

RD
[...]

QA ...
DS ...

RT{
TraceName.SCF matchElsewhereHighQual phrap 825 860 20080619:133013
}

RT{
TraceName.SCF matchElsewhereHighQual phrap 870 1002 20080619:133013
}

The CT tags are consensus tags and might appear somwhere in the ACE file
AFAIR, but mainly put at the end.

Consed is very sensitive concerning (missing) empty lines, you should
separate the (CT,RT) tags by one line.

just another 2p,
Sven


2009/5/28 Bastien Chevreux <bach@xxxxxxxxxxxx>

> On Mittwoch 13 Mai 2009 Lionel Guy wrote:
> > On 13 May 2009, at 23:01 , Bastien Chevreux wrote:
> > > Do you mean that tags for reads (RT) must be at the end of each contig
> > > together with contig tags (CT)? What happens for ace files with
> > > multiple
> > > contigs?
> >
> > Nope, worse (in my opinion). All tags (CT and RT) for all contigs and
> > reads must be at the very end of the file, after the last read of the
> > last contig. I'm away from my files now and couldn't test it
> > completely, but I just copied a bunch a CT tags from the first contig
> > to the end of the file, and they magically appeared when I fired
> > consed...
>
> Hi Lionel,
>
> I'm a little bit puzzled. From what I could find in available consed
> documentation on the ACE format, everything should be right and I can't
> find a
> viable reason why consed can't load the tags.
>
> Could you please contact the consed developer and see what they have to say
> on
> that topic?
>
> Regards,
>   Bastien
>
>
> --
> You have received this mail because you are subscribed to the mira_talk
> mailing list. For information on how to subscribe or unsubscribe, please
> visit http://www.chevreux.org/mira_mailinglists.html
>

Other related posts: