I am quite new to Staden, but mainly interested in mutation detection function.
When comparing trace display output from Contig Editor, I've found obvious difference between 1.4 beta version (v2003.0b1) and the new one - there was more background noise left from substraction of sequences in the new one. I've tried different setings but could not reduce thas noise. It seems there should be some change in programing algorithm. Does anyone has any help suggestions?
I cannot recall which version of the various trace subtraction algorithms was in place with each particular release, but yes there have been changes to the algorithms.
However unfortunately this is largely now unsupported code (as I do not have the time to further develop the mutation detection code other than to fix obvious bugs).
The very earliest versions used to automatically adjust for Y-scale changes. This should still be available.
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