Size Standard Normalization Feature; File Name Conventions Library; File Name Convention Overview - Thermo Scientific appliedbiosystems SeqStudio Flex Series User Manual

Chapter 11 Manage library resources on the instrument
11

File Name Conventions library

Size standard normalization feature

For fragment analysis applications, the software includes an optional normalization feature for use
with the GeneScan
with instrument, capillary array, sample salt load, and injection variability between capillaries and
instruments. Normalization can be applied during data collection.
Based on the settings specified in the run module and the data collected for GeneScan
Standard v2.0, the software calculates a normalization factor for each sample based on a threshold
setting. The normalization factor is used as a multiplier to adjust the peak height of the sample peaks
relative to the GeneScan
IMPORTANT! Normalization is not applied to samples with failing sizing quality. Select a size standard
definition file appropriate for your application that accurately sizes samples. For example, if your
application includes small fragments that may be obscured by primer peaks, or large fragments that
may not be present due to slower migration rates, specify a size standard definition file that eliminates
these fragments from sizing.
To use the normalization feature:
• Prepare each sample with the GeneScan
• Use a run module with optimized normalization settings (see the normalization settings as
described in "Run module settings"
• Select the appropriate normalization size standard in the plate file (see "Size standard definition
files provided"

File Name Conventions library

File name convention overview

A file name convention specifies the naming convention for sample data files.
If you do not specify a file name convention for a plate, the following default file name conventions are
used:
• Sequencing—Well_Sample_TimeStamp
• Fragment analysis—Well_Sample_SampleType_TimeStamp
278
™ ™
600 LIZ Size Standard v2.0. This feature attenuates signal variations associated
™ ™
600 LIZ Size Standard v2.0 peaks.
on page
on page 275).
SeqStudio ™
™ ™
600 LIZ Size Standard v2.0.
273).
Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide
™ ™
600 LIZ Size