How to create a metadata table
Table of Contents:
Step 1: Download the metadata table template
Step 2. Enter sample names under “SampleName” (column A)
Step 3. Enter file names under “Filename” (column B)
Step 4. Edit experimental variable(s) (column C – column n)
Step 5. Update the “Strandedness” column
Step 6. Update the “LibraryLayout” column
Step 7. Upload your metadata table!
There is important data about your samples, also known as metadata, that is necessary to collect for them to be analyzed successfully in Trovomics. However, this information is not included in your sequencing files. To ensure we have the minimum required metadata for your samples, we created a metadata table template to organize your samples’ metadata. A metadata table describes your samples that the RNA was isolated from and is requirement for creating an experiment in Trovomics. Your metadata table will dictate what comparisons are available to you when you start an analysis for an experiment. Therefore, your metadata table will influence differential gene expression analysis and plot visualization.
Objective: Create a metadata table for an experiment in Trovomics.
Pre-requisites: If you already have a metadata table created for your RNA-Seq experiment, then this would be beneficial to use as a starting point. The Trovomics automated RNA-Seq pipeline requires, at minimum: sample names, FASTQ file names, and desired experimental variables. If you do not have an existing metadata table, use the list below to collect information on your samples and their sequencing files (FASTQ):
| Metadata Field | Required? | Definition | Comments |
|---|---|---|---|
| Sample Name | Yes | A unique identifier for a sample | We recommend naming your samples based on their accompanying file names, so it is easy to keep track of what files belong to what sample. |
| File Name | Yes | The full name of the FASTQ file | File names should be in the original format as received from your sequencing provider. For more information on accepted FASTQ file names, visit our FAQ. |
| Experimental Variable(s) | Yes | An attribute that differs between different samples in your experiment. Examples include:
|
You will need at least one experimental variable in your experiment, with at least two values to make a comparison e.g., An experimental variable of “sex” with values “male” and “female” meet the minimum requirement. |
| Library preparation methods | No* | Parameters associated with how your RNA samples were sequenced such as RNA selection method, strandedness, and sequencing read-type | *Since these parameters are selected during experiment creation, they are not required in your metadata table. |
TIP: Need help preparing your metadata table? One of our computational biologists can assist you via a Trovomics Consultation! Every paid plan comes with included consultation hours to help you get started!
Step 1. Download the metadata table template
We recommend downloading our metadata table template which can be accessed during the Build Your Experiment Step in Create Experiment (Image 1). Using our template will help ensure your metadata table is in the correct format.
Image 1. Click the icon (arrow) to download the metadata table template at the Build Your Experiment step in Create Experiment.
Our template looks like this (Image 2):
Image 2. Trovomics’s metadata table template.
The “SampleName” and “Filename” column titles are required to be in your table and should not be altered. Information under these columns need to be accurate for your sample metadata to be mapped to the correct sample file(s).
Step 2. Enter sample names under “SampleName” (column A)
First, identify how many sequencing files each sample has. The number of files each sample has will dictate how many rows are needed for each sample. If your sequencing read type was single-end, you would have 1 file per sample and each sample name would need to be pasted into 1 row under the “SampleName” column. If it was paired-end, you would have 2 files per sample and each sample name would need to be pasted into 2 rows (Image 3).
TIP: We recommend deriving your sample name from your file names so that they are easily identifiable.
Step 3. Enter file names under “Filename” (column B)
Enter the full file name(s) in the “Filename” column for each sample, as they were received from your sequencing provider. In the previous step, we have already designated how many rows to dedicate per sample based on the number of sequencing files provided per sample. If you have only 1 file per sample, then you will only have 1 file name to assign for each sample. If you have 2 files per sample, then you will have 2 file names to assign for each sample (Image 3).
Image 3. Single-end sequencing read types will only have one FASTQ file per sample (left). Paired-end types will have two FASTQ files per sample (right). Duplicate the your sample name in another row to accommodate another FASTQ file name.
Step 4. Edit experimental variable(s) (column C – column n)
The default experimental variables in our template are “Disease” (values = control, disease), “Age” (values = 41, 43, 50, 52, 53, 55), and “Organism” (value = Homo sapiens) (Image 1). However, these can column titles can be replaced with variables unique to your experiment. Additional columns can be added to accommodate additional variables (Image 4). The more variables you enter, the more comparisons you will be able to analyze in Trovomics so think about what groups you would like to compare in an analysis when setting up your metadata table.
Image 4. Insert columns in the table to add more experimental values to your metadata. Rename the default “Disease”, “Age”, and “Organism” columns as necessary, or delete if not needed.
TIP: The table is highly case sensitive. Use consistent naming conventions throughout the table. For example, if you are describing samples as “13 weeks”, do not enter variations such as “13 week” or “13 w”. Label them all as “13 weeks”.
Step 5. Update the “Strandedness” column
The values under the “Strandedness” column title are defaulted to “unstranded”. Change this to “forward” or “reverse” for all samples, depending on your sequencing sense.
Step 6. Update the “LibraryLayout” column
The values under the “LibraryLayout” column title are defaulted to “Single”, which designates a single-end sequencing read type. Change this to “Paired” if your sequencing read type is paired-end.
TIP: Ensure you have no blank cells within your metadata table. Each cell should be filled within the confines of your table. Any blank cells will impact how your samples are processed in Trovomics.
Step 7. Upload your metadata table!
Your metadata table is now complete and ready for you to upload during experiment creation (Image 5).
Image 5. An example of a completed metadata table for Trovomics.