Downloading Data from the exRNA Atlas

There are several different options for downloading data from the exRNA Atlas.
You can either download data on an individual, sample-by-sample basis, or you can download data in bulk.

Downloading Individual Core Result Archives

Take a look at the following faceted search grid (certain metadata columns are hidden for this example):

You can click the icon for any given sample to download its core results archive.
This core results archive contains all of the most important files generated by the exceRpt pipeline, including all of the read mapping documents to various libraries.

Downloading Individual Raw FASTQ Data Files

Alternatively, if you want to download the raw FASTQ data file associated with a given sample, take a look at the following faceted search grid:

You can see three different icons in the highlighted column:
  • The icon indicates that the raw FASTQ file is openly available for download.
    This icon will only be present if the dataset is already available in a public domain archive like SRA or GEO.
    Simply click the icon to download the raw FASTQ file.
  • The icon means that the data is restricted access and is currently under the protected period (embargo).
    The embargo on this dataset will end 12 months after the time the data was submitted to the DCC. View the ERC Consortium Data Access Policy for more details.
  • The icon means that the data is deposited in the controlled access dbGaP archive.
    You can click the icon under the Actions column to view the dbGaP Study Id. You can then contact the PI through dbGaP to get access to the raw FASTQ data files.

Downloading Datasets in Bulk

If you want to download result files in bulk for a given search, you can click the Download Samples button at the top of the grid, as seen below:

You can then choose between four different options.

The Download All Core Result Files link will download a tab-delimited file that contains information on how to download the processed core results archives for each sample.

The Download All Result Files link will download a tab-delimited file that contains information on how to download the full results archives for each sample.
These archives can be very large (gigabytes), so we recommend that you start by downloading the core results archives (which are usually around 3-5 MB).

The Download All Raw Data Files link will download a tab-delimited file that contains information on how to download all available raw sequencing data files in FASTQ format.
These FASTQ files are only available for samples that are open access.
You can tell which samples have available FASTQ files by looking for the icon in the Download Data column.

These tab-delimited files will contain two separate columns:
  • The first column contains the names of the different samples.
  • The second column contains the URLs to actually download the files.

There are several ways of downloading the files in your tab delimited list:

  1. You can copy and paste each URL in your browser and hit Enter to download each file in this list.
  2. For more advanced users, you can use a command line program like wget to download these files.
    • wget -O {FILE NAME in Column 1} {URL in Column 2}, or
    • curl --output {FILE NAME in Column 1} {URL in Column 2}
    • Replace {FILE NAME in Column 1} with the actual file name in Column 1, and replace {URL in Column 2} with the actual URL in column 2.

In order to download one of these tab-delimited files, you must agree to the ERC Consortium Data Access Policy, which pops up in a new window.
This same policy can also be found at the top of each tab-delimited file.

Downloading Metadata

The Download Metadata link in the Download Samples menu will download the biosample, donor, and experiment metadata documents associated with a single sample.
All metadata documents will be placed in a single text file.
Before downloading your metadata, you must select a single sample by using the checkboxes to the left of each sample in the grid.
Multiple sample selection is currently not allowed.

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