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Apply Metadata to FastQ Files

Description:

Here we make use of the Data Store's ability to tag files with metadata. Many of these metadata descriptions will be required for submission of data to a repository prior to publication. We will modify the previously downloaded 'SraRunTable.txt' on our local computer in a spreadsheet program and then upload to the Discovery Environment and link these descriptions to the files. This process of metadata application can be applied to any dataset in the Data Store and is a recommended practice.

Tip

If you were using this tutorial with your own data, uploading your FastQ files and continuing from this section would be a recommended starting point. See the |Data Store Guide| for more information about uploading files to the Discovery Environment.

Input Data:

Input Description Example
FastQ files (e.g. SRR9666131.sra.fastq,SRR9666132.sra.fastq…) Sequencing data in FastQ format |SRA FastQ Files|

Apply Metadata

1. In a spreadsheet program (e.g., Excel), open the SraRunTable.txt file on your local computer.

Tip

Renaming the file with a '.csv' extension before opening the file may make it easier for your spreadsheet program to properly interpret.

  1. To the spreadsheet, add a new first column (left-most). Name this column “file.”
  2. At this point, sort the spreadsheet by run (ascending). This will make it easier in the subsequent steps when file names will likely be alphanumerically sorted.
  3. In the file column we will list the path in the Data Store for each FASTQ file as corresponds to its accession in the Run column. (e.g., /iplant/home/USERNAME/rna-seq-tutorial/fastq_files/ SRR9666132.sra.fastq). In the Data view, clicking the three dots next to any file/folder icon reveals a function menu which includes an option to Copy Path.

Note

Your first two columns should be similar to the below (with your username replacing username below:

File Run /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666131.sra.fastq SRR9666131 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666132.sra.fastq SRR9666132 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666133.sra.fastq SRR9666133 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666134.sra.fastq SRR9666134 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666135.sra.fastq SRR9666135 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666136.sra.fastq SRR9666136 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666137.sra.fastq SRR9666137 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666138.sra.fastq SRR9666138 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666139.sra.fastq SRR9666139 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666140.sra.fastq SRR9666140 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666141.sra.fastq SRR9666141 /iplant/home/username/rna-seq-tutorial/fastq_files/SRR9666142.sra.fastq SRR9666142

5. (Optional) At this point, you can add any desired additional columns with any metadata you want to add. For our tutorial this is not necessary.

  1. Save this file as fastq_file_metadata.csv on your local computer.

7. In the Discovery Environment Data view, navigate to the metadata folder in your rna-seq-tutorial folder. Open the folder and then click the Upload button, then select Browse Local.

  1. Browse your local computer to select the fastq_file_metadata.csv; upload the file. You will get a notification when upload is completed. You may need to refresh your browser to see the uploaded file.
  2. In the Data view, navigate to your rna-seq-tutorial folder and select (checkbox) the fastq_files folder.
  3. Click the More Actions button and select Apply Bulk Metadata. Browse to and select the fastq_file_metadata.csv file in the metadata folder. Click Done to complete this action. You will get a notification when the metadata has been applied successfully.
  4. To view the metadata, navigate to the fastq_files folder and select (checkbox) any individual FASTQ file. Click the More Actions button and select Metadata. You will then see the applied metadata. You can build custom search queries on any of these attributes (column names in your original spreadsheet) and the values (the entries for these columns). See |Data Store Guide| for more information about advanced search queries and smart folders.

Output/Results

Output Description Example
fastq_file_metadata.csv A CSV file containing metadata labels for the FastQ files |FastQ metadata|

Description of output and results

With metadata applied, this files are now more easy to search and organize. These metadata properties will also be of use in data submission to repositories like SRA.

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