Exploring an SRA entry

Overview of an SRA entry

The SRA (Sequence Read Archive) provides access to unassembled data (Figure 41). Accession numbers starting with 'ER' are assigned by EBI, while those starting 'SR' are assigned by NCBI and 'DR' by DDBJ. In other words, the original database the sequence was submitted to is identifiable by these two letter codes. This is important, because with SRA sequences submitted to EBI (ER entries) you can access both the original sequence as submitted by the author as well as normalized sequence data as 'Fastq Files'. By contrast, when using ENA to view SRA sequences submitted to NCBI (SR entries) or DDBJ (DR entries), you can only view the 'Fastq Files'. 

SRA entry ERP000001

Figure 41. SRA entry ERP000001.

Notes

[A] Summary provides general information on the submitted sequence and its source.

[B] Tabs section the SRA data for ease of handling:

  • Navigation provides links to related SRA data (see next section);
  • Fastq Files provides links to download normalized SRA sequence data (see 'Exporting SRA sequences and data'); 
  • Submitted Files provides links to download SRA sequence data as submitted by the author (see 'Exporting SRA sequences and data');
  • References provide links to literature cited in the entry.

[C] The tab shown is the 'Fastq Files' tab with cross-links to individual studies and sequence downloads.

 

Help

More information on SRA entries can be found here.

 

SRA entry - Navigation tab

The Navigation tab allows you to explore all the Sequence Read Archive data associated with an entry. In this way you can browse SRA data by sample, experiment or run, and even see the original submission data (Figure 42).

SRA entry ERP000001 showing the Navigation tab

Figure 42. SRA entry ERP000001 showing the Navigation tab.

Notes

[A] Down arrow allows you to navigate down through a tree in order to explore Sample, experiment or run SRA data.

[B] Back arrow allows you to navigate back to the original SRA submission data.

[C] For example, by following the link to ERS000001-ERS000012, you will have a list of the twelve SRA samples associated with entry ERP000001.

SRA entry - References

Literature references relating to the SRA sequence are provided under the References tab (Figure 43). Cited literature should be considered as a pointer to scientific information and not a credit for the elucidation of the sequence.

SRA entry ERP000001 showing the References tab

 Figure 43. SRA entry ERP000001 showing the References tab.

Notes

[A] Abstract can be expanded to view the abstract.

[B] Links are provided to the full paper as a html, pdf, doi or as a cross reference to CiteXplore.