Applied Biosystems 3500 User Manual

Setting
Description
Clear range methods
• Use clear range minimum and maximum—Specifies the first and last
base in the range to consider, or trims the specified number of bases
from the 3¢ end.
• Use quality values—Sets a window with a specified number of allowed
low-quality bases by removing bases until there are < X number of bases
per Z number of bases with QV < Y.
• Use identification of N cells—Sets a window with a specified number of
allowed ambiguous base calls (Ns) by removing bases until there are < X
number of Ns per Y number of bases.
Basecalling protocol—QV settings
Setting
Description
Contiguous Read Length The longest uninterrupted segment of bases with an average Quality Value
(QV) ³20.
In addition to evaluating the QV of a base call, the software considers the QV of
adjacent bases within a ±21-bp moving average to determine a contiguous read
length based on quality values.
Trace Score The average basecall Quality Value (QV) of bases in the clear range sequence of a
trace.
The clear range is the region of the sequence that remains after excluding the low-
quality or error-prone sequence at the 5¢ and 3¢ ends. The clear range is calculated
by the KB basecaller using QVs.
QV20+ The total number of bases in the entire trace with Quality Value ³20.
Sizecalling protocols library (primary analysis—fragment)
A sizecalling protocol is the required primary analysis protocol for fragment
applications.
A sizecalling protocol denes peak detection, sizing, and quality values.
When you create a fragment assay, you add a sizecalling protocol to the assay. If you
add this item from the library, a copy of the item is added to the assay, and can be
modied independently from the original item stored in the library. For information
on how changes are tracked if auditing is enabled, see “Audit action“ on page 205.
Sizecalling
protocol overview
Chapter 7 Manage library resources
Sizecalling protocols library (primary analysis—fragment)
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3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1

Applied Biosystems 3500 Specifications

General

Number of capillaries	8
Capillary Length	50 cm
Laser	Solid-state laser
Instrument Type	Capillary electrophoresis system
Technology	Capillary Electrophoresis (CE)
Weight	95 kg
Power Requirements	100–240 V