Create an analysis protocol
An analysis protocol contains all the settings necessary to analyze sequencing data.
1.
In the navigation pane of the Data Collection Software, select GA
Instruments
4
ga3730
4
Protocol Manager.
1
2
1
Instrument Protocols
2
Analysis Protocols
2.
Click New in the Analysis Protocols pane.
3.
Edit the settings as needed. See “Analysis protocol parameters“ on page 89.
4.
Click OK.
Analysis protocol parameters
Option
If checked, the software creates…
Sequence File Formats
• Write SEQ File—A SEQ file for printing the sequence as text file or for using the file
in other software.
– ABI format that is used with Applied Biosystems
™
software.
– FASTA format that is used with other software
• Write Standard Chromatogram Format file (SCF) —When selected, the software
creates a SCF file that can be used with other software. The SCF extension is not
appended to the file name.
• Write Phred (PHD.1) File —When selected and the KB
™
basecaller is used, the
software creates a PHD 1 file that can be used with other software.
Basecaller and Dye Set
Select the appropriate Basecaller and DyeSet/Primer based on the chemistry and
capillary array length you are using.
Chapter 7
Create and manage instrument protocols, run modules, and analysis protocols
Create an analysis protocol
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3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide
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