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STADEN Unwated format conversion

jkb at mrc-lmb.cam.ac.uk jkb at mrc-lmb.cam.ac.uk
Fri Feb 15 09:24:12 EST 2002

In <3C6BB282.A20FE40B at bbsrc.ac.uk> Simon Andrews <simon.andrews at bbsrc.ac.uk> writes:

> I've got a problem with using ABI files (*.abd) with Staden 2001, which
> wasn't a problem with Staden 2000.

I'm sure this would have been a problem with the 2000 release too.

> I'm trying to pass the files through pregap without reformatting them
> into SCFs, ZTRs or anything else.  The problem is that if I use any kind
> of base calling algorithm on them, then I get a format conversion I
> didn't ask for.  If I use Estimate Base Accuracies it turns them into
> ZTR files (and links these to the exps), and if I use Phred it makes
> them into SCFs.

Please take up this issue with ABI. The reason why everyone writes to SCF is
simply that SCF is a public standard with example source code freely
available. ABI on the other hand is a proprietary format closely guarded by
ABI. People reverse engineered enough to extract the bits needed, but
generally most people have more than enough sense than to write back to this
format - they'll switch to something more standard.

At one stage I had a phone call from ABI asking if we had software for
converting from SCF to ABI, as they needed such a tool. I took great pleasure
in saying how would I do that - you've never given us your file format
specifications? There was a long pause (filled in my imagination by the sound
of shooting oneself in ones foot). Anyway, it transpired that even though they
wanted us to write an SCF to ABI converter they were still unwilling to tell
us more about the format!

Is there a reason why you need to write back to ABI format files? They're large
compared to SCF and huge next to ZTR.

> In the Trace format conversion module there is an option to delete
> temporary files used as part of base calling - but what do I do if I
> don't want to convert format at all (and hence this module is
> uninitialised)?

The delete temporary files is there in case more than one round of format
conversion is done.

Eg ABI (input) -> SCF (from phred) -> ZTR (convert trace). In this case the
SCF files are redundant as we can regenerate them from the input files (ABI -
not deleted) and they're not the final output either.

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Fax: (+44) 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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