Searching SRA

Search for Reads in SRA searches the NCBI SRA database for entries with metadata matching the query terms you provide. The sequences and metadata for selected runs can be downloaded. Alternatively, just the metadata for the selected runs can be saved for use later.

Search for Reads in SRA uses NCBI's e-utilities, which occasionally experience downtime. If searches unexpectedly return no results, go to to check the status of the service.

Start Search for Reads in SRA by going to:

        Download | Search for Reads in SRA (Image download_reads_ncbi_sra_16_n_p)

Image srasearchdialog
Figure 10.5: "Accession" was selected from the drop-down menu of search fields, and a single accession was entered. The results of the search include the run with the accession provided, as well as runs submitted to SRA as part of the same experiment.

Search fields

A drop-down menu at the top left lists the fields that can be searched (figure 10.5). Generally, all search terms provided must be present in an SRA entry for it to be returned. Within a single search field, OR can be added between terms to indicate that just one of the terms needs to match. The exception to this is the Accession field, which is described further below.

Details about selected search fields:

SRA search results

A table with one row per result is returned. The columns to display in the table can be configured in the side panel, on the right.

Details about selected column contents:

When a run is selected in the table, the title and abstract for the SRA experiment it is part of is displayed in the SRA Preview tab, under the column configuration section of the side panel.

Please refer to the SRA documentation at the NCBI for full information on the data and metadata available

Further details about download and import of data from SRA, including information on file sizes and paired read handling, is provided in Downloading reads and metadata from SRA.

The total number of experiments found is reported at the bottom of the search table. An experiment may have more than one run associated with it.

By default, up to 50 results are retrieved at a time. Click on the more... button below the table to pull additional results, 50 at a time. This number can be configured in Preferences:

        Edit | Preferences (Image Options_3_16_n_p) | General | Number of hits (NCBI/Uniprot)

Right-click on a row in the results table to get a list of possible additional searches, based on the selected run (figure 10.6).

Image srasearchmore
Figure 10.6: The SRA search result table.