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

  • From: Arnaud Ungaro <arnaud.ungaro@xxxxxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 2 May 2012 15:32:55 +0200

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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