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Set Analysis Parameters

1 Open RNA Amplicon from BaseSpace Sequence Hub as follows.
    a Select the Apps tab, and then select RNA Amplicon.
    b From the Version drop-down list, select 1.0.0.
    c Select Launch Application.
2 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.

3 Select Select Project(s).
4 Select a project to store app results to, and then select Select.
5 From the Custom Manifest File field, select the manifest file for analysis.
6 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.

7 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.

8 From the Biosamples section, identify a sample group as follows.
    a Enter a preferred name in the Label field.
    b Select Select Biosample(s).
    c Select the checkbox of each biosample you want to analyze, and then select a prep kit you want to use with the biosample.
    d Select Select.

You can set up multiple groups to hold each set of replicates, eg, for biological replicates.

9 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.

10 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.

For Research Use Only. Not for use in diagnostic procedures. 

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