Frequently Asked Questions

This page provides answers to frequently asked questions about the DNAnexus SRA site

General Questions

What is the SRA powered by DNAnexus?

The DNAnexus SRA site is hosted by DNAnexus and allows you to search and filter all the publicly accessible Sequence Read Archive data available at http://www.ncbi.nlm.nih.gov/sra, with the exceptions of the Sequence Reads Archive Analyses data and the Trace Archive repository. More specifically, it includes all of the data from the NCBI SRA site for studies, experiments, samples, and runs.

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Do I have to pay anything for using the DNAnexus version of SRA?

No, the DNAnexus hosted SRA is freely available to all researchers for data browsing and data download.

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Can I upload and store sequence data onto the DNAnexus SRA site?

The DNAnexus hosted SRA site does not currently allow researchers to upload and store their own sequence data.

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How can I search the data archive on the DNAnexus SRA site?

The search capabilities implemented allow you to quickly find any study, experiment, sample, or run of interest. You can search over multiple annotations and terms for any of the objects in the SRA database. Simply type any number of search terms into the provided search box in the object’s page of interest, e.g. search for “human” and “Broad institute” in the “Studies” tab (see example below) and review the ranked list of returned results.



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What functionalities are available to me to browse the returned search results on the DNAnexus SRA site?

There are multiple ways to navigate through the returned search results.

  1. Filter search results – utilize the available filters shown to the left of the results table. The filters listed are driven by the content in the results table, meaning they reflect the information listed that can be filtered on. Selecting a set of filters and sub-filters will refine the content in the results table.



  2. Related objects button – understand how many and what type of experiments, runs, or samples are for example associated with one or many studies returned. Select the rows (e.g., studies) of interest and view the related objects by clicking the appropriate “Related objects” button. Related objects are listed in a results table in a new page.



  3. Inline information for specific objects – obtain additional information for one or many specified object(s) by opening additional information available inline within the search results table by clicking the ► icon.



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How exactly do the filters work?

The filter menu to the left of your results table allows you to refine your results based on a number of different annotations for the data in your results table. The filters listed are driven by what your search has returned in the results table making them much more specific to your inquiry. Selecting a set of filters and sub-filters will refine the content in the results table in real-time. Filters include among others, organism, sequencing type (e.g., Epigenetics, RNA-Seq, among others), submitter, instrument, platform, and whether the data has been published or not. The filters shown are the top five by frequency for each category with the option to “See all”.

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Questions about Download

In what format can I download the data?

All SRA data can be downloaded in the SRA format as provided by the Archive.

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How do I download data files?

First select the object(s) you would want to download in one of the search results views, followed by clicking the “Download” action button (Note: In all cases, the “runs” for the selected objects will be considered for download.).

This will bring you to the Download page where you can download one or multiple data files.

  1. Download a single data file – You can download a single reads archive data file from the Downloads page in SRA format, by clicking the appropriate download button in the “Download” column for the run of interest.
  2. Download multiple data files – You can download one or many reads archive data files from the Download page, by selecting the different runs you intend to download. Next, download the urls as a txt file by clicking the appropriate action button above the table. The downloaded txt file lists the urls for all the different files selected.
    1. You can either fetch one file at a time by copying and pasting the provided urls into your browser, or if you are familiar with command-line you can download the specified files using this methodology which allows multiple large data download of all the files selected (please also see What tools do you recommend for downloading large data files).
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What else do I need to know when downloading files from the DNAnexus SRA site?

Downloading large files may take a while and is dependent on your network connection. If you are using your browser to download the file and your connection is interrupted during your download, you will probably need to restart the download from the beginning. To alleviate these issues, we suggest using a download manager or download accelerator. These tools can download files much faster than your browser alone by downloading each file in multiple parts simultaneously and they can allow you to resume an interrupted or cancelled download.

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What tools do you recommend for downloading large files?

The NCBI recommends using Aspera for downloading large files. Please see the Aspera Transfer Guide for more information.

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