Fine-tune your web-based search results with SRA Run Selector

Run Selector is a tool available through the Sequence Read Archive (SRA) that allows you to fine-tune your web-based search results. There are over two dozen fields that can be used to filter SRA data in Run Selector. For example, if you need to look at data from a particular sequencing platform and genome assembly, you can use these fields as filters.

After running a web-based search for any keyword in the SRA database, users can dump all the results (up to a maximum of 20,000 experiments) into the Run Selector for fine-tuning. In addition, Run Selector shows you how many runs fall into each of the categories even before a filtering category is selected, allowing you to investigate the data further by noting what is contained within the database.

post 2 fig 1 run results
Figure 1. After searching with SRA, click on “Send to” to open the drop-down menu. Then click on the radio button labeled “Run Selector” to send your search results to Run Selector. Note that you can already see how many runs are in each of the categories to the left.

For instance, searching SRA for “cardiac” brings up 3,095 records. This is a small enough set to automatically send to the Run Selector, but we can still narrow it down to contain the specific type of data you’re interested in. Let’s say you’re looking for DNA data – specifically, whole exome sequencing data. Selecting DNA from the web search narrows the results further.

post 2 fig 2 after running selector.png
Figure 2. After filtering the results, we can see all the relevant runs.

After setting filters for Assembly Name (grch37), Assay Type (wxs), and Platform (illumina), there are 1,596 runs remaining, and they are all from the same BioProject (PRJNA183422). Clicking on the hyperlinks inside the data table will take you to the NCBI page for that SRA Study or BioProject.

You also have the option of downloading the data from the table or just downloading the accession list; the download buttons for each are directly above the table. The table and accession list are downloaded as simple text documents, but the data table download is tab delimited and can be opened in Excel.

We hope you’ll find this resource helpful and beneficial to your research needs. If you have questions or comments regarding Run Selector, please email and we’d be happy to help!

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