FASTA and FASTQ files may be uploaded via the REST API or by using the One Codex CLI or Python client library. The latter two options are simpler and thus recommended (and also support automatic interleaving and validation of your FASTA/Qs). In every case, we replace spaces in filenames with underscores. To upload with the CLI, simply: 
# If you haven't previously logged in, the following command
# will prompt you for your username and password and then
# save a ~/.onecodex file with your API key
onecodex login

# This command will automatically upload all FASTQs into your account,
# prompting you to interleave any paired end data (recommended) if applicable
onecodex upload $LIST_OR_GLOB_OF_YOUR_SAMPLES
Uploading via the REST API consists of 3 steps:

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Samples over 20GB

The REST upload above only allows sample uploads up to 20GB (optionally compressed with gzip). If you need to upload a compressed file over 20GB, please use the onecodex CLI.