[mira_talk] Re: Hybrid EST assembling (Two species, A and B, Backbone from A, solexa sequences from B)

  • From: Surya Saha <ss2489@xxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 2 May 2012 09:51:54 -0400

In that case convert_project is guilty :-) Try running it with the "-r C"
flag.

"convert_project -r C -f caf -t html project_out.caf project"

Hope this helps.

-Surya

On Wed, May 2, 2012 at 9:32 AM, Arnaud Ungaro <
arnaud.ungaro@xxxxxxxxxxxxxxxxx> wrote:

> I use "convert_project" to visualise the assembly
> "convert_project -f caf -t html project_out.caf project"
>
>
> Also mira generates a fasta with IUPAC letters the assembly folder:
> ./project_assembly/project_d_results/project_out.padded.fasta
>
> I also tried "convert_project -f caf -t fasta project_out.caf
> project", always IUPAC letters
>
> Thanks
> Arnaud.
>
> 2012/5/2 Surya Saha <ss2489@xxxxxxxxxxx>:
> > Hi Arnaud,
> >
> > How did you generate the consensus, i.e. what alignment tool did you use?
> > There are no IUPAC letters in your debris reads so IUPAC's were not
> > introduced by MIRA but by the aligner.
> >
> > -Surya
> >
> >
> > On Wed, May 2, 2012 at 5:38 AM, Arnaud Ungaro
> > <arnaud.ungaro@xxxxxxxxxxxxxxxxx> wrote:
> >>
> >> Hi ! Thanks a lot, your tips were useful !
> >>
> >> A lot of sequences hits on the backbone. But I have a little problem
> >> .. I surely miss use a good parameter. I see many locus different from
> >> backbone, they are congruent, but consensus is weird, contains IUPAC
> >> letters instead of the congruent letter.
> >>
> >> I tried deactivate IUPAC with "fnicpst=yes" but I got the same thing.
> >>
> >> Here an screeshot of the alignment :
> >> http://arnaud-ungaro.fr/img/mira020512.png
> >>
> >> Thanks , Arnaud
> >> ......
>
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