Beckman Coulter CEQ 8000, User Manual

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Fragment Analysis Procedures
248 CEQ™ 8000 Genetic Analysis System
STR Locus Tag Editor - Allele ID Criteria
The
Allele ID Criteria
tab contains the parameters used to accurately identify your
alleles and to set these “true” alleles apart from various other anomalies identified in
the fragment list.
A sample fragment is identified as representing a particular allele if its apparent size is
found to be the very similar to the size of a particular allele fragment in the allele list.
However, because the mobility of a fragment is affected by both its sequence and its
size, the nominal allele size will not likely be the same as its apparent size. Therefore,
the system identifies the alleles based on their “closeness” to an apparent size. This is
carried out by the system using a user-defined confidence level.
Confidence Interval
The confidence interval is automatically generated as a result of the bin analysis, but
can also be entered manually by the user. When automatically generated, the value
displayed is dependent on the overall standard deviation computed in the bin analysis
and the user-specified confidence level (default = 95%). When the confidence interval
is manually entered by the user, the system uses the entered value and the confidence
level to estimate an overall standard deviation.
Increasing the confidence interval will have the effect of increasing the width of the
bins.
The confidence interval should be set to a value less than 0.5 nt.
If a value of zero is entered into the confidence interval field, the system uses only the
standard deviation of the estimated sample fragment size in the statistical test used to
identify a fragment as corresponding to an allele.
When the confidence interval is user-entered, the allele identification will not
correspond to an error probability estimated from actual data but will still be a useful
relative indicator of the “goodness” of the match.
1. Select the
Overwrite system generated value
check box if would like to
overwrite the confidence interval value generated by automatic binning.
2. If you are overwriting the system generated value, specify a confidence interval
(number of nucleotides (+/-)) in the
Allele confidence interval
field.