Sequencing Analysis Software v7.1, initial license - FAQs

Please download this PDF (https://downloads.thermofisher.com/Sequencing_Analysis_Software_v7.1/100107870_SeqA_v7.1_Release_Notes.pdf).

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.

The primary updates for Sequencing Analysis Software v7.1 (SeqA 7.1) are the following:

- Sequencing Analysis Software v7.1 (SeqA 7.1) is supported only on Microsoft Windows 10 Professional/Enterprise operating system
- Sequencing Analysis Software v7.1 (SeqA 7.1) supports data generated from SeqStudio Flex Series Genetic Analyzers
- Sequencing Analysis Software v7.1 (SeqA 7.1) uses KB Basecaller version 1.4.2.6 for basecalling
- Sequencing Analysis Software v7.1 (SeqA 7.1) supports upgrade from Sequencing Analysis Software v7.0

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.

Sequencing Analysis Software v7.1 supports data generated from the following Applied Biosystem instruments:

- SeqStudio Flex Series Genetic Analyzers
- SeqStudio Genetic Analyzer
- 3500 Genetic Analyzer
- 3500xL Genetic Analyzer
- 3130 Genetic Analyzer
- 3130xl Genetic Analyzer
- 3730 DNA Analyzer
- 3730xl DNA Analyzer
- 310 Genetic Analyzer

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.

When editing sample files by inserting or deleting bases in Sequencing Analysis software, the change will be reflected in the .seq file after the changes have been saved. It is not necessary to re-analyze the samples. In fact, re-analyzing the samples will remove any changes made to the sample file. If the changes had been made and saved and you inadvertently re-analyzed the samples, do not save the file. Remove it from the sample manager without saving and add it to the sample manager again to restore it to its last saved version.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.

In the Sequencing Analysis software, a standard chromatogram format (.scf) file is compatible with Staden package.

Note: When standard chromatogram file format is created, the .scf extension is not appended to the file name. However, the file format is correct.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.

The Mobility File can be changed in a number of locations in the Sequencing Analysis software :

Sample Manager: Change the Mobility file in the DyeSet/Primer column by selecting another Mobility File from the pull down menu. You can make the same change for all the samples by making the change in the first sample, then click on the column name to select the column. Go to Edit and select Fill Down.

Analysis Protocol: If changing the Mobility File for 1 sample, you can make the change in the Analysis Protocol by selecting the row number for the sample you wish to change, going to the Analysis menu and selecting Analysis Protocol. Select the Basecalling tab and make the change there.

Analysis Manager: If changing the Mobility File for multiple samples, you can do that by applying a new Analysis Protocol or changing an existing one. To do so, go to the Analysis Menu and select Analysis Protocol Manager. Click once on the Protocol you wish to modify and select Edit, or select New from the menu choices on the bottom of the panel. Go to the Basecalling tab and make the changes. If creating a new Analysis Protocol, make any other appropriate changes to the other tabs. When finished, press OK. At this point you can either select "Apply to All Samples", which will apply the changes to all samples in the Sample Manager, or "Apply to Selected Samples", which will apply the changes to the samples that had been selected.

Once the changes have been made, select the BC column and re-analyze your samples.

Note: When changing the Mobility File, make sure that the Mobility File and the Basecaller match. For example, if using the KB Basecaller, make sure that you are using the KB Mobility Files. If they do not match, analysis might fail.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.

In the Sequencing Analysis software, the differences in the ABI and KB Basecallers are the following:

The ABI Basecaller analyzes data using an algorithm from previous versions of the ABI PRISMSequencing Analysis Software.

The KB Basecaller has the following features:
* Calculation of mixed bases: Mixed bases are one-base positions that contain two bases. These bases are assigned the appropriate IUB code.
* Calculation and display of quality values (QVs) for pure and mixed bases. The QV is a per-base estimate of the basecaller accuracy.
* Option to call Ns when the quality threshold is not met.
* Option to process data with true or flat profile.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.

The different User Categories in the Sequencing Analysis software and their privileges are the following:

Analyst
* View, customize, export, and print the Analysis Report.
* Add and remove samples to and from the Sample Manager.
* Print Sample files views.
* Change the Basecaller, Mobility, and Matrix (where applicable) files in the Sample Manager.
* Insert, delete, or change bases in the electropherogram or sequence views.
* Text Searches.
* Edit the Sample Name.

Scientist
Can do everything in the Analyst category, plus:
* Create or edit an existing Analysis Protocol (either from the Analysis menu or from the Analysis Defaults) and apply it to a set of samples.
* Delete an Analysis Protocol.
* Set the Clear Range determination.
* Edit the Display Settings.

Admin

Can do everything the Scientist and Analyst can do, plus:
* Create or inactivate User Accounts.
* Import or export User Accounts.
* Turn the Timeout feature On or Off.
* Turn the Audit Trail feature On or Off.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Software Support Center.