Section IV: Sequence Analysis FAQ Sheet
36
CEQ™ 8000 Series Genetic Analysis System
I have sufficient Raw Data signal but I didn't get a base call.
What can I do?
In certain cases, the base calling algorithm cannot find the start of data. If this happens,
a default start time is automatically used. The default time is determined by a
combination of the separation method parameters (voltage, temperature, and voltage
ramping profile) and the length (33cm or 53cm) of the capillary used to collect the
data. This may not be the optimal starting point for the data.
Sometimes simply by setting the start of data manually, samples can be analyzed
accurately. To manually set the start of data, expand the raw data near where the initial
peaks are seen. Examine the data and look for a peak that is DNA (i.e. not
unincorporated dye terminators, which will usually be the first eluted peaks and be
very large and broader than the DNA peaks) and has a sharp profile. Reanalyze the
data using the center of this peak as a start time.
Including peaks from unincorporated dye terminators in the data to be ana-
lyzed may result poor basecalling results in as many as the first 50 called
bases. If it appears that such peaks have adversely affected the basecalling,
try setting the start time later than the unincorporated dye terminator peaks.
