You can download raw FastQ files by clicking Download FASTA/Q within the results page for each sample. If you have sequenced your samples with us, or if you have a premium account, the option to download will be displayed below the Compare Sample tile:
If you have paired-end data in two separate files (R1 and R2), once they are uploaded to the platform, we interleave those files. This means that both R1 and R2 files are combined into one file, with sequence 1 from the R1 file followed by sequence 1 from the R2 file; then sequence 2 from R1 file, and so on.
Downloading Multiple Samples:
To download multiple samples at once you will need to install the One Codex API - Python Client Library and CLI. This can be done following the instructions here: https://github.com/onecodex/onecodex
The bulk download method described here is using the Command Line Interface (CLI).
Once installed, check your onecodex version. The bulk download of samples is only supported in versions v0.10.0 and above.
onecodex --version
Next you will need your API Key. This can be found by selecting the account name in the top right corner, then settings. Alternatively using the CLI you login by entering:
onecodex login
This will prompt you to enter your account email and password.
Now you should be ready to download samples using the command:
onecodex --api-key [API_KEY (optional if already logged in)] download samples [Options: --help, --tags TEXT, --project TEXT, --prompt, --no-prompt] [output directory]
An example command downloading all files in the project BATCH1 to the current directory would look like:
onecodex --api-key YOURKEYHERE download samples --project BATCH1 ./
If you are still having trouble downloading your samples, reach out to us by email (support@onecodex.com), or by clicking on the chat icon at the bottom-right of your screen. We're happy to help!