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> - You can specify the same condition in column 2 and 3 to perform only the first part of the secondary analysis (all but comparisons). If you do so, make sure that there is only one line in your file.
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> - The first condition column is the test and the second is the control
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### Select samples and override sample conditions
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If you need to select samples or override some sample conditions and/or factors, you can do so by specifying a new samplesheet with the `-s` option.
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The samplesheet needs to be a tab separated file with two or three columns:
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- first column: samples that you want to select
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- second column: new condition of the sample
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- third column(optionnal): new factor for the sample
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| :--- | :--- | :--- |
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| sample1 | conditionX | factor1 |
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| sample2 | conditionX | factor2 |
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| sample3 | conditionY | factor2 |
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| sample4 | conditionY | factor1 |
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> **Note:**
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> - Conditions specified here must correspond to the comparisons file described above.
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> - Conditions specified will override the ones described in the configuration files of the project folders
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> - Factors specified will override the ones described in the configuration files of the project folders
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> - If you need to override factors without changing the conditions of the samples, you will still have to specify the conditions in the second column.
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## Running the pipeline
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:one:
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