Using the SRA Run Selector

The Run Selector can select runs from one or more studies to download or analyze with the SRA Toolkit.

Search Bar

At the top of the page is the Search Bar 1. SRA Run Selector search parameters are accessions of the studies, samples or experiments like the one below. Multiple studies can be included by using a comma separated list of study accessions.

• Studies:

  • SRA Study accessions (prefixes SRP, DRP, ERP)

    Examples: SRP000002, DRP000617, ERP002000

  • BioProject accessions (prefixes PRJNA, PRJDB, PRJEB)

    Examples: PRJNA111397, PRJDB90, PRJEB1976

  • dbGaP study accessions (prefix phs)

    Example: phs000159

  • GEO Study (prefix GSE)

    Example: GSE12578

• Samples:

  • SRA Sample accessions (prefixes SRS, DRS, ERS)

    Examples: SRS000013, DRS000020, ERS000016

  • BioSample accessions (prefixes SAMN, SAME)

    Examples: SAMN00000013, SAMEA774460

  • GEO Sample (prefix GSM)

    Example: GSM769008

• SRA Experiment(s)

  • SRA Experiment accessions (prefixes SRX, DRX, ERX)

    Example: SRX000002,SRX000003,SRX000004

Facets

Selectable filters called facets can be used to find rows of interest.

Facet Selection 2: In the "Facets" panel, check the box next to name of a facet to enable it.

Facet 3: Checking the box 4 will include a value in the filtered set. Multiple filters can be used. The number to the right of filter values is the run count that will be added or removed.

Common fields 5

The common field are values shared by all runs in the set and not useful for filtering. The common fields can be hidden by clicking "Hide common fields".

Result table 6

The “# runs found” is the total of runs matching all filter criteria currently selected. The list will be displayed on multiple pages if more than 100 runs match

Columns can be sorted by clicking the column’s heading 7. The first click will sort in ascending order, the second click column will sort in descending order, and a third click will turn off column sorting. Currently only one column at a time can be sorted.

Selection table 8

The ‘Total’ line lists the number and size of all runs in the current search

• Accession List: will provide a list of selected run accessions and can be used with the SRA Toolkit. using the --option-file <accession list file>.
• RunInfo Table: will provide a tab delimited table of all runs and attributes in the current search.

Individual runs can be added to the selected list by clicking the checkbox, this will also highlight the run in green 9. Unchecking the box next to a run will remove it from the list of selected runs.
Clicking this button will add all runs matching the current filter criteria to the selected runs list.
Clicking this button will remove all runs that match the current filter can be removed using this button.