[mira_talk] Re: paired_end

Hi all,
following this topic.
When I have my multifasta splitted...assembled..converted to gap4...
I can not look at the flowgrams because gap4 can not find READNAME.f
or .r or .pl simply because the name is just thereal name in sff file is
READNAME and can not open trev with anoder modified name. 
Somebody know how to workout with this problem?

Thank you

Giuseppe

On Tue, 2009-04-14 at 16:40 +0200, Lionel Guy wrote:
> Hi Jan,
> 
> On 14 Apr 2009, at 16:08 , Jan Paces wrote:
> 
> > Unfortunately it looks like it
> > is not possible to download .sff files from NCBI trace archive  
> > anymore,
> > they are offering only fasta or fastq
> 
> You can access some of them via ftp, but I don't know how long it's  
> going to last:
> ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/
> 
> >  I know rns parameter, but how to set up
> > insert size?
> 
> 
> I think there are some other utilities in the third-party tools of  
> mira, although I don't know how they work. AFAIK, I have split my  
> reads, using .r and .f suffixes. The xml file then resembles:
> 
> <?xml version="1.0"?>
> <trace_volume>
>      <trace>
>          <trace_name>FLVI58L05FSYNS.r</trace_name>
>          <insert_stdev>3000</insert_stdev>
>          <insert_size>20000</insert_size>
>          <clip_vector_right>94</clip_vector_right>
>          <template_id>FLVI58L05FSYNS</template_id>
>          <trace_end>r</trace_end>
>      </trace>
>      <trace>
>          <trace_name>FLVI58L05FSYNS.f</trace_name>
>          <insert_stdev>3000</insert_stdev>
>          <insert_size>20000</insert_size>
>          <clip_vector_right>62</clip_vector_right>
>          <template_id>FLVI58L05FSYNS</template_id>
>          <trace_end>f</trace_end>
>      </trace>
> ...
> </trace_volume>
> 
> Hope that helps...
> 
> Lionel
> 
-- 
Dr. Giuseppe D'Auria

Cavanilles Institute for
Biodiversity and Evolutionary Biology
University of Valencia
"Poligono de la Coma" s/n
46980 Paterna (Valencia),Spain

web: http://www.uv.es/cavanilles/genevol/
tel: +34 9635 43646



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