Beckman Coulter CEQ 8000, User Manual

Page: 167 / 382

Analyzing Sequence Data
User’s Guide 153
To specify the threshold, enter the desired value, between 0.00 and 1.00, in the N
Threshold text box. A value of 0.99 will call all peaks as indeterminate (N’s) except
the high quality peaks. A value of 0.50 will call only the lowest quality peaks as ‘N’s.
A value of 0.00 will not call any peaks as ‘N’s. The value of 0.60 is the recommended
starting threshold. Subsequently, the threshold and/or the stringency of your alignment
tool should be adjusted to suit your needs.
After setting the N Threshold, the data must be reanalyzed.
If you had set a N Threshold of 0.99, out of 100 bases called as ‘N’s, 99
of those would have been correct. The higher the N Threshold, the
higher the number of correct bases will be called as ‘N’s. Again, it is
important to set the N Threshold properly, as good quality data is lost
when the N Threshold is set too high.
Click
OK
. Any called bases or regions of data that have a Call Score below the
specified threshold will be called as ‘N’s.
Analysis Start
Enter the time in minutes from the start of raw data to the time when data analysis is to
begin. The range is 0.0 to 180.0 and the default is 0.0.
An entered Analysis Start or Stop time will override any automatically
determined start or stop time. In addition, if you enter a stop time that
exceeds data collection time, analysis will terminate at the end of data
collection.
Analysis Stop
Enter the time in minutes from the start of the raw data to where data analysis will end.
If an Analysis Stop time is entered and PCR Product (used to deter-
mine the end of analyzable data) is checked, the system will use the
earlier of the two stop times to conclude the analysis.
PCR Product
This check box indicates that the sample was generated from a PCR product and
signals the system to end analysis when a sudden drop of signal lasts for more than
two minutes. This prevents the analysis of baseline data.
<200 Bases
This field is enabled when the
PCR Product
option is checked. This feature has been
included to allow for the sequencing of shorter fragments.