Prepare Experimental Design Metadata for Sleuth¶
Description:
Before we use Sleuth to analyze our data, we need to create a tab-delimited file that matches our samples to their conditions. It is convenient to do this on your local computer, using a spreadsheet program. We can easily modify the SraRunTable.txt file we downloaded from the SRA.
Input Data:
| Input | Description | Example |
|---|---|---|
| Metadata from the SRA | Metadata that describes our dataset; will be modified to appropriately indicate experimental variables and controls. | SraRunTable |
Create Experimental Design Table¶
1. In your spreadsheet program, open SraRunTable.txt (downloaded previously from SRA).
2. According to the Sleuth instructions, the first column must be named 'sample'; rename the Run column to sample.
3. Next, you will want to create new columns which specify attributes about each sample such as what treatment/condition correspond to each sample. In the table below, we suggest columns that indicate the condition (e.g., control, NAA treated, high-melatonin, low-melatonin), replicate numbers, etc. See the example experimental design file for the example of the file to create.
4. Save the experimental design file in TSV format (e.g. experimental_design.tsv).
5. In the Discovery Environment, navigate to the metadata folder you created for this experiment (rna-seq-tutorial/metadata). Click the Upload button and select Browse Local.
6. Browse your local computer to select the experimental design file (i.e., experimental_design.tsv) and upload the file. You will get a notification when upload is completed. You may need to refresh your browser to see the uploaded file.
Output/Results
| Output | Description | Example |
|---|---|---|
| experimental_design.tsv | A TSV file describing how each sample relates to an experimental condition and/or metadata variable. | Example experimental design |
Description of output and results
The TSV file created links the name of the sample (in our case synonymous with SRA accession numbers) to the experimental design (e.g. conditions, controls, and other metadata).