utilizing sequence quality scores results from new ABI basecaller

James Bonfield jkb at mrc-lmb.cam.ac.uk
Thu May 1 06:46:12 EST 2003


MEC at Stowers-Institute.org ("Cook, Malcolm") wrote in message news:<CED81D34E37D5043A1211565277A51E59F7EA5 at exchkc02.stowers-institute.org>...
> Is is possible to configure staden pregap4 somehow to utilize the quality scores now available from ABI's new KB basecaller that are embedded in the ab1 files?
> 
> The net effect I suppose would be to transfer them as AV values into the .exp files without having to call phred.

This is possible to add - I think it's the CONF field in the ABI files. I may
have a look at this at some stage, but anyone else should feel free to look at
it too. This is in io_lib, and that bit's been an open source part of the
package for many years.

Could you put an example file up on the web/ftp somewhere so that I, or others,
can download it and see what it would entail?

James




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