Set Analysis Parameters
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1
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Open RNA Amplicon from BaseSpace Sequence Hub as follows. |
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a
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Select the Apps tab, and then select RNA Amplicon. |
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b
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From the Version drop-down list, select 1.0.0. |
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c
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Select Launch Application. |
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2
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To override the default analysis name, enter a preferred analysis name in the Analysis Name field. |
The default is the app name with the date and time the session was started.
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3
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Select Select Project(s). |
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4
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Select a project to store app results to, and then select Select. |
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5
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From the Custom Manifest File field, select the manifest file for analysis. |
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6
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To enable gene-based normalization, select the Enable Gene-Based Normalization checkbox. |
DESeq2, by default, uses all the amplicon targets to perform library-size normalization. When this option is enabled, only the amplicon targets targeting the provided genes are used for normalization.
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7
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If you selected the Enable Gene-Based Normalization checkbox, enter preferred gene names in the Gene Name(s) field. |
Make sure that you separate gene names with a semicolon.
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8
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From the Biosamples section, identify a sample group as follows. |
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a
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Enter a preferred name in the Label field. |
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b
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Select Select Biosample(s). |
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c
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Select the checkbox of each biosample you want to analyze, and then select a prep kit you want to use with the biosample. |
You can set up multiple groups to hold each set of replicates, eg, for biological replicates.
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9
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Select Add a New Row to add as many groups that you want to analyze. |
Pairwise differential expression is performed between all pairs of groups.
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10
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Select Launch Application to start the analysis. |
When analysis is complete, the status of the app session is automatically updated and you receive a confirmation email.
BaseSpace RNA Amplicon v1.0 App Online Help
For Research Use Only. Not for use in diagnostic procedures.