[mira_talk] Re: clipping in sff_extract

On Dienstag 19 Mai 2009 Schafleitner, Roland (CIP) wrote:
> I tried to extract sequence, quality and traceinfo files from sff files
> using sff_extract and at the same time clipping 6 bases from the left
> end using the -min_left_clip=6 command in sff_extract to correct for the
> wrong clipping performed by the sequence provider. MIRA however cannot
> load the resulting files, as the number of bases per read in the
> sequence and qual files seem not to be identical anymore.
> Has anybody an idea how to overcome this problem?

Hi Roland,

can you please have a look at the newest version of sff_extract that Jose 
uploaded? (http://bioinf.comav.upv.es/sff_extract/download.html)

It should solve your problem.

I think you bumped into the same problem of malformed SFF files as other people 
did. I made a quick fix and sff_extract is now prepared for that eventuality.

Regards,
  Bastien

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