SRA search options
Search parameters
Fields that can be searched are listed in a drop-down menu on the left hand side (figure 8.5). All fields is the default option, but specifying particular fields to use can provide more relevant results. Fields where some explanation is of benefit are listed below.
Terms provided in each of the search fields must all be present in an SRA entry for that entry to be returned. (I.e. queries use AND between the terms.) Within a single query term, OR can be added to indicate that each term should be searched for individually. For example: searching in the Accession field for SRR20016268 SRR20016241 SRR20016341 would not return anything, as the query is interpreted as SRR20016268 AND SRR20016241 AND SRR20016341 and no single entry in SRA contains all 3 accessions. However SRR20016268 OR SRR20016241 OR SRR20016341 would return 3 entries.
- Accession See the example above for searching for multiple accessions. Note that searches for an SRA accession may return additional runs submitted as part of the same experiment. To retrieve all runs in a study, provide the study accession as the query term.
- Modification/Publication date Find entries modified/published within a date range, specified as [MM] [YYYY]. For example, a publication date given the following range
08 2016 to 08 2016would return results published between the first and last days in August 2016. - Strategy Select from a drop-down list of types of experiments e.g., RNA-Seq, ChIP-Seq, etc.
- Library Selection Select from a drop-down list of known library preparation methods, e.g. Poly(A), Size fractionation, etc.
- Platform Select from a drop-down list of NGS sequencing platforms e.g., Illumina, Ion Torrent, etc. Note: Download of data from some platforms, such as Complete Genomics, is not supported.
- Instrument Select from a drop-down list of individual NGS sequencing machines e.g., HiSeq X Ten, Ion Torrent PGM, etc.
- Paired Status Select Paired or Single, for paired or single end runs respectively.
- Availability Select Public or dbGaP. The latter contains confidential data. Entries in dbGAP can be searched and metadata for entries returned can be saved, but reads cannot be downloaded directly. Access to dbGAP involves an application to the NCBI.
- PubMed Select "has abstract" to find entries with a PubMed abstract or or "has full-text article" for entries where the entire publication is available.