[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 15:31:34 -0400

Yes, you could do that. Can you also look into the quality of the last base
on those reads? That could be tipping things in favor of the reference for
the caller.

-Surya

On Wed, May 2, 2012 at 10:08 AM, Arnaud Ungaro <
arnaud.ungaro@xxxxxxxxxxxxxxxxx> wrote:

> Well saw :-) !
> Things are getting better, but a weird thing appears.
>
> Let see here : http://arnaud-ungaro.fr/img/mira020512-2.png
>
> In exemple, at  the last locus ,the majority of reads are T, but consensus
> set to A (same as backbone).
>
> Maybe by setting backbone's quality lower ?
>
>  Thanks for your help
>
> 2012/5/2 Surya Saha <ss2489@xxxxxxxxxxx>:
>
> > 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.
> >> ...
>

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