SRA Data Format Frequently Asked Questions

How can I get original quality scores if I need them for my analysis process?

The SRA toolkit uses the SRA Normalized Format with full base quality scores by default, so to continue getting original quality scores in your output files you don't need to change anything. If you have previously set the Prefer SRA Lite files with simplified base quality scores option on the main page of the toolkit configuration, simply unset that option and save the configuration to resume using SRA Normalized Format by default.

Is it expensive to access data in the cloud in comparison to on premises?

As long as you are working in the same region as the data then accessing the files is free. You would only pay storage costs for keeping the data on your disk, we have more details available in this outline that should be considered.

Is all SRA data available in SRA Lite format?

Eventually yes, though it will take time for existing archives to be converted to the new format, during which only some runs will be available in the SRA Lite format. If you set the Prefer SRA Lite files with simplified base quality scores
option on the main page of the toolkit configuration, this will instruct the tools to preferentially use the SRA Lite format when available.

What is the file extension for SRA Lite files?

The SRA Lite has a .sralite file extension, while the SRA Normalized Format files will continue to have a .sra file extension so they can be easily distinguished by filename.

How can I estimate my cloud cost in GCP or AWS for storage and computation?

Google Cloud Platform (GCP) and Amazon Web Services (AWS) both have developed pricing calculators that users can use:

• GCP: https://cloud.google.com/pricing
• AWS: https://calculator.aws/#/

Where can I find SRA Lite test data?

To see an example of the output for this data format, or to compare it to the SRA Normalized Format for the same accession, please use these runs as an example:

SRR1091086
SRR1107478
SRR1105693
SRR1068355

After setting the Prefer SRA Lite files with simplified base quality scores option on the main page of the SRA Toolkit ( version 2.11.2 or later) configuration, you can proceed with your normal SRA toolkit operations on these runs to see SRA Lite format in action.

Engage

NCBI wants your feedback on SRA in the Cloud. Contact sra@ncbi.nlm.nih.gov with questions or if you would like to provide input on new functionality.