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)
³
20.
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
³
20.
Sizecalling protocols library (primary analysis—fragment)
A sizecalling protocol is the required primary analysis protocol for fragment
applications.
A sizecalling protocol defines 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
modified 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)
7
178
3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1
