[mira_talk] Re: bug

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


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