When a sequencing install standard run completes successfully, the CRL Pass/Fail
row displays green or red results.
For each capillary:
1.
Click a capillary to display the spectral and raw data proles for a capillary
.
2.
Check that the data meet the following criteria:
Attribute Acceptance Criteria Example
Order of the peaks in the spectral
pr
ofile (intensity vs pixel) from left to
right
4-dye: blue-green-yellow-red
Extraneous peaks in the raw data
pr
ofile (intensity vs scan)
None
Note: The E5 profile may include
extraneous peaks outside the matrix
peak region, which can be ignored.
E5:
Extraneous peaks in the raw data
pr
ofile (intensity vs scan)
None
Peak morphology in the spectral
pr
ofile (intensity vs pixel)
• No gross overlaps, dips, or other
irregularities
• Peaks separate and distinct
• Peak apexes are separate and
distinct (the tails will overlap)
3.
(Optional) Review the CRL Basepair Accuracy to determine discrepancies from
the reference sequence.
If y
ou observe large discrepancies (for example, 5–10 contiguous miscalled bases
in the middle of a sequence), review the data. If you see a raw data peak larger
than the adjacent peaks with baseline pull-up in all 4-dye color channels, it may
indicate the presence of a bubble. Check the pump, run the Remove Bubbles
wizard (see “Remove bubbles from the polymer pump“ on page 237), then
repeat the run as needed.
4.
If the data for the required number of capillaries meets the criteria above (at least
7 capillaries for 8-capillary instruments, at least 22 capillaries for 24-capillary
instruments), click Accept Results.
Evaluate
sequencing install
standard data
Chapter 6 Run c
alibrations and install checks
Run a Sequencing install check
6
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3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1
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