A Sample represents an underlying next-generation sequencing (NGS) data file, either in the form of a de-multiplexed FASTQ or a FASTA file. Often, there will be a single sample for each physical specimen, though in some cases there may be multiple Samples for each individual specimen (e.g., in the case of replicates).
Samples should be in FASTA or FASTQ format, optionally gzipped, and may be up to 20GB in size. Uploading samples requires 2 direct API calls, one to start the upload and a second to actually POST the FASTA or FASTQ files. If you need to upload a compressed file over 20GB in size, please contact us for help at [email protected].
The below table summarizes all of the properties for the Sample resource, with the JSON schema type of each property listed below in italics. Details on how to upload your NGS data, as well as retrieve and modify your Samples follows.
|The sample ID encoded as an addressable URI|
|Timestamp for when the sample was created on the One Codex platform, encoded as a RFC 3339 timestamp|
|The sample filename (e.g., "sample.fastq")|
|The size of the uploaded file in bytes.|
|Samples may be |
Note: Samples imported via an external service (e.g., BaseSpace) may also be marked as
|A reference to the user that uploaded and owns the sample, e.g., |
|A reference to a sample's accompanying Metadata, e.g., |
|A reference to the (optional) Project containing a sample. Samples can be part of zero or one projects.|
|A reference to a Classification for the sample. This will typically be the One Codex Database or Targeted Loci Database results as appropriate. Note that samples will not have a |
array of strings
|An (optionally empty) array of references to Tags describing the sample. Tags are an additional unstructured organizational tool that complement Project and Metadata records.|