Obtain Accession Numbers and Metadata from the SRA¶
Description:
In this section, we will describe how to import data from the NCBI Sequence Read Archive (SRA). The example dataset is available at the SRA under the accession PRJNA553702. It is not possible to directly download sequencing files from the SRA. Instead, we must obtain the accessions for the individual sequencing files and use the 'sra-tools' software to download those files.
Get SRA Accession Metadata¶
- Go to the SRA.
- Enter the BioProject accession 'PRJNA553702' in the search bar and press Search.
- This search should return 12 entries which are individual sequence files associated with this experiment. Click on any of the results (e.g., GSM3936272: 100µM MEL rep3; Arabidopsis thaliana; RNA-Seq). This will lead to a page with a detailed description of the experiment.
- Under the Study heading, find the link to All runs and click this to access the SRA Run Selector. (Direct link: SRP214076)
- Under the Select heading, there are two downloads (simple text files) available for download. Click on Metadata and Accession list to download both files. The metadata file will be called SraRunTable.txt and the accession list will be called SRR_Acc_List.txt.
Note
All metadata and accession lists from the SRA will have the same file names. Be sure to rename or carefully organize these files if you will be downloading other SRA data.
Output/Results
| Output | Description | Example |
|---|---|---|
| SraRunTable.txt | Metadata from the SRA | SraRunTable |
| SRR_Acc_List.txt | Accession list from the SRA | SRR_Acc_List |
Description of output and results
The SraRunTable.txt will be used to label our files using the Data Store\'s metadata capabilities. We will use the SRR_Acc_List.txt as input for importing files from the SRA.