Set Analysis Parameters
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1.
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Open the RNA-Seq Differential Expression app from BaseSpace Sequence Hub as follows. |
- Select the Apps tab, and then select RNA-Seq Differential Expression.
- From the Version drop-down list, select 1.0.0.
- Select Launch Application.
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2.
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To override the default session name, enter a preferred session name in the App Session Name field. |
The default is the app name with the date and time the session started.
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3.
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From the Save Results To field, select Select Project. |
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4.
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In the Select Project dialog box, select where to store app results, and then select Select. |
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5.
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From the Reference Genome drop-down list, select the reference genome that was used during alignment. |
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6.
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If a custom genome was used during alignment, select Select Datasets from the Custom Genome field, and then select the custom genome used during alignment. |
The labels of this field and button in the software interface might be different from the labels in this guide, depending on the BaseSpace Sequence Hub mode.
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7.
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From the Strandedness drop-down list, select the strandedness of the samples specified in the alignment app. |
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8.
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If an enrichment panel was used during alignment, select it from the Panel drop-down list. Otherwise, select None. |
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9.
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[Optional] Select the Enable Differential Expression Analysis checkbox to perform differential expression analysis between two groups of samples . If selected, both control and comparison datasets must be specified in the App Result Groups section. |
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10.
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[Optional] Select the Perform Paired-Sample Analysis checkbox to perform paired-sample analysis between two groups of samples . |
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11.
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To override the default control group label, enter a preferred label in the Control Group Label field. |
The default is control.
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12.
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To override the default comparison group label, enter a preferred label in the Comparison Group Label field. |
The default is comparison.
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13.
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Select Select Datasets to specify the RNA-Seq Alignment App data for the analysis. |
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14.
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In the Select Datasets dialog, drag each dataset you want to use as the control in the analysis to the Control Samples drag and drop area. |
The selections made in the Filters for RNA-Seq Alignment App Results section affect which datasets are displayed in the Select Datasets dialog box. If you do not see the datasets you want to use in the analysis, make sure that your filter selections match the settings used in the RNA-Seq Alignment app.
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15.
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[Optional] If you are performing differential expression analysis, drag comparison datasets to the Comparison Samples drag and drop area. |
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16.
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[Optional] If you are performing paired-sample analysis, make sure each control dataset is paired with a comparison dataset in a row. |
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18.
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Select Launch Application. |
When analysis is complete, the app updates the status of the session and sends you an email notification.