[mira_talk] Re: bug

Dear Burkhard, Laurent and Bastian
 
In my hands the 05.05 version of sff_extract gives bad quality files
only if clipping commands are given. Just running sff_extract yields
qual, fas and xml fils that are readily accepted by mira.
R
 
On Dienstag 05 Mai 2009 Burkhard Steuernagel wrote:
> Hi Laurent,
> did you use the sff_extract third party script? I had exactly the same
> error for some of my SFFs and it turned out that the sff_extract
script
> produced wrong data.
> Once upon a time there was the command
> sffinfo mysff.sff |sffinfo2mirafiles.tcl -project mysff
> and applying this on the same sff worked good.
 
Yikes! This is something I'd actually like to hear earlier. sff_extract
is 
actually quite good and as long 454/Roche does not offer the possibility
to 
split paired-end reads of a SFF, it's the only possibility I know to get
these 
sequences out of the container.
 
Actually, there has been some work don on sff_extract and I'm waiting
for Jorge 
to put it up on his web site.
 
Burkhard, can you please have a look at
    http://www.chevreux.org/tmp/mira_3rdparty_05-05-2009.tar.bz2
and tell whether the version contained within still produces wrong
results for 
you?
 
If yes, I'd need to wield a debugger and go out on a hunt.
 
Regards,
  Bastien
 

 

 

Roland Schafleitner

PhD, Biotechnology Research Scientist

Germplasm Improvement and Crop Enhancement Division

International Potato Center - CIP

Avenida La Molina 1895, Apartado 1558

La Molina, Lima 12, Peru

Tel.: +51 (0) 1 349 6017, annex 3065

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