[mira_talk] Re: paired_end

On Tuesday 14 April 2009 Giuseppe D'Auria wrote:
> 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?

I do (at least I think so :-)


Hello Guiseppe,

the problem at the moment is that 454 sequences and stores one read for each 
sequence pair. BTW, they're the only one to do that ... and also to have still 
the linker in the read. One of the reasons why working with 454 paired-end is 
not trivial.

Now, as workaround, "sff_extract" splits the reads and stores them as FASTA. 
The clean way would be to also re-create a completely new SFF file that mimics 
the data as it is stored in the fasta files ... including stored flowgrams. I 
think it shouldn't be too difficult to realise but I currently have absolutely 
no time.

So, if you know a informatics / bioinformatics student ... that would be a 
nice little thing to implement :-)

Sorry I cannot give you a more satisfactory answer.

Regards,
  Bastien



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