Set Analysis Parameters

Set Analysis Parameters

1 In BaseSpace, click the Apps tab.
2 Click Amplicon DS.
3 From the drop-down list, select version 1.2, and then click Launch to open the app.
4 In the Analysis Name field on the input form, enter the analysis name. By default, the analysis name includes the app name, followed by the date and time that the analysis session starts.
5 From the Save Results To field, select the project that stores the app results.
6 From the Targeted Amplicons field, select a panel of targeted amplicons representative of the selected samples.
7 If you selected Custom Manifest in the Targeted Amplicons drop-down list, upload a custom manifest and select the manifest file from the Custom Pool A/B Manifest File field. Upload a custom manifest as follows.
    a Navigate to your project in BaseSpace.
    b Click Import.
    c Follow the instructions to add the Custom Amplicon manifest file (*.txt) to the project.

Note

By default, the Amplicon DS App uses the Smith-Waterman algorithm for alignment and the Somatic variant caller.

8 From the Annotation field, select a preferred gene and transcript annotation reference database.
9 From the Sample Pairs field, select the samples for a pooled sample pair. Select the samples as follows.
    a Click Select Pairs to open the Select Pairs window.
    b [Optional] Search for the samples you want to analyze.
    c Select a sample from the search results, or click Select All to select all samples, and then drag and drop the samples to the appropriate location (Pool A Samples or Pool B Samples).
    d Click Confirm.

Note

Select matching pooled sample pairs.

10 Click Continue.

The Amplicon DS App begins analysis of the sample.

When analysis is complete, the status of the app session is updated automatically and an email is sent to notify you.