Important Notes on Download Facilities

A number of users have asked why SRA does not provide data in their format of interest.

• The SRA does not have the resources to develop format conversions for all possible formats that users may wish. In any case, these formats often have multiple versions and change quickly as new bioinformatics tools and methods become popular.
• Instead, one basic format (SRA) is provided by the Archive for all publicly available data. A toolkit is also provided that supports conversion to several popular formats. The toolkit is also easily extended to supply data in other formats.
• The SRA is a high throughput resource that relies on streaming output. For this reason certain file types that require indexing or that require evaluation of the data stream in order to know how best to compress it cannot be served efficiently. This is the reason that SRF is not supported.
• Users are advised to switch from ftp to aspera for bulk downloads. Aspera provides: faster bandwidth, higher level flow control, user level encryption, and ability to download trees of components.

Related Documents

NCBI Large Data Download Best Practices

Notices

Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government, and shall not be used for advertising or product endorsement purposes.

Conventions Used in this Document

../itemThe location of the item will be specific to the user’s installation.

<item>The items inside the angle brackets are user supplied.

[item]The item inside the square brackets is optional.

{item1|item2}The user must select one of the options inside the curly brackets.

Software Version

This guide is current to SRA Toolkit version 2.1.6 released September 10, 2011. Instructions for previous versions of the SRA Toolkit may be different from those provided in this guide. We recommend that users stay current with SRA Toolkit updates to benefit from feature additions and bug fixes.

Filtering and Selection

In the Run Browser, you can filter and subset reads according to certain regular expression pattern matching:

• Sequence substring: one of the biological reads for a spot should contain the substring
  Examples: ATTGGA, ^ATTGGA, ATTGGA$, ATGDNNAT, ATGGA&GCGC
  See "SRA nucleotide search expressions" for more details.
• Name of a spot you are looking for.
  Example: EXWA4RL02G9Z6H
• Name of a spot plus a window in pixels around it.
  Example: EXWA4RL02G9Z6H X=100 Y=100 - will return all spots located within 200 pixels (in X and Y) from a given spot.

Downloading Data from the Run Browser

You can download data from one or more runs in an SRA Experiment in fasta form and a simple fastq form that has none of the treatments of the static fastq dump. The download dataset will however reflect the filtering and selection you may have performed.

Format of Run Browser Data

The Run Browser supports IUPAC basespace and colorspace base data. The quality scores are in the Phred scale with 0 being at ASCII character 33 or ‘!’. Reads can be viewed combined or seperated using the customize options in the Run Browser.

Aspera Connect

Due to the potential for large SRA archive sizes, we recommend that users install and exercise the Aspera Connect client when possible. There is no cost associated with installing the Aspera Connect plug-in. Aspera Connect can be used either as an internet browser plug-in or as the command-line program ascp. Additional information about Aspera can be found in the Aspera Transfer Guide or by visiting Aspera documentation for ascp.