Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

4
Chapter 4 View Reports
View overall run reports
Parameter Normal Run Problematic Run
Failed panels In general, the number of failed panels
should be relatively small and
consistent.
Fraction of Best +
Good
beads/Usable
beads
Effective exposure
times
The fraction can vary depending on
the quality of the library, the efficiency
of the PCR, and the enrichment
process. As a guideline, the fraction is
around 0.5 to 0.6 in the first ligation
cycle of each primer and drops to 0.2
to 0.3 in the last cycle.
Gradual increase from ligation cycles
1 to 5 or higher for each sequence
primer. Performance varies from slide
to slide and as a function of the age of
the SOLiD Light Source. As a
guideline, the effective exposure time
is typically 20 to 40 ms in the first
ligation cycle and increases to 100 to
300 ms in the fifth cycle.
Satay plots The first cycle of any primer should
show a relatively “clean” Satay plot,
with most points clustered on the four
color axes and with minimal fraction of
the points clustered around the origin.
The quality of the Satay plot typically
degrades gradually with each ligation
cycle for a single primer cycle,
becoming more “fuzzy” in the last
cycle.
Run begins with extremely high
number of failed panels or dramatic
increase in any subsequent ligation
cycle for each sequencing primer.
A significant drop in the fraction of
good beads in the initial ligation
cycles is a reason to pause the run
and troubleshoot the performance.
250 ms or greater in ligation cycle 1 or
when instrument times out when the
effective exposure time exceeds 500
ms. Long exposure times may
indicate replacement of the SOLiD
Light Source.
An abnormal “fuzzy” Satay plot in the
first cycle is a reason to pause the run
and troubleshoot the performance.
70 Applied Biosystems SOLiD 4 System SETS Software User Guide