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using naming schemes

Jolyon Holdstock j.holdstock at oxagen.co.uk
Tue Apr 29 03:12:05 EST 2003

Dear All,

I have a query about the use of naming schemes in Staden version 1.3
I have set up a SNP detection pipeline to run with PolyPhred and PolyBayes
as well as the default trace difference and het scan modules.
If Staden is run without PolyBayes and without PolyPhred, and with a naming
scheme, then it works with forward and reverse reads being recognised.
However if PolyPhred and PolyBayes are included along with a naming scheme,
then many files are lost with the error:
 Error: Failed file filename.exp written to error file
Running the pipeline with PolyBayes and with PolyPhred, and without a naming
scheme results in few files failing.

This would suggest that the naming scheme is affecting the process but I
don't know how. Does anyone have any ideas/experience of this?


Jolyon Holdstock

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