Running TruSeq Amplicon
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If you are analyzing TruSeq Custom Amplicon samples, and the manifest file is not yet uploaded to BaseSpace, perform the following: |
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Select the manifest file for the panel you used in selection. |
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Click the Apps button.  |
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Find TruSeq Amplicon in the list and click the Launch button. |
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If you see the End-User License Agreement and permissions, read them and click Accept if you agree. |
Now you can fill out the required fields in the TruSeq Amplicon input form.
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Analysis Name: Provide the analysis name. Default name is the app name with the date and time the app session was started. |
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Save Results To: Select the project that stores the app results. |
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Sample(s): Browse to the sample you want to analyze, and select the checkbox. You can select multiple samples. |
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Targeted Amplicons: Select the panel you used for selection. |
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Custom Manifest File: Select the TruSeq Custom Amplicon manifest file for analysis. This option is only available when Custom Panel is selected in the Targeted Amplicons drop-down list). |
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Variant Caller: Choose which variant caller to use. |
Note
The Somatic Variant Caller is recommended for TruSeq Amplicon - Cancer Panel and TruSight Myeloid Sequencing Panel samples.
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Annotation: Choose which gene and transcript annotation reference database to use. |
Figure 2 TruSeq Amplicon Input Form
The TruSeq Amplicon app now starts analyzing your sample. When completed, the status of the app session is automatically updated, and you receive an email.
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