Sequence file

A file of read sequences generated by a sequencing experiment.

Properties

INSDC run accessionsequence_file.insdc_run_accessions (array) An International Nucleotide Sequence Database Collaboration (INSDC) run accession. For example "SRR0000000".

Lane indexsequence_file.lane_index (integer) The lane that this file was sequenced from. For example "1".

Library preparation IDsequence_file.library_prep_id (string) A unique ID for the library preparation. For example "tech_rep_group_001".

Read indexRequiredsequence_file.read_index (string enum) The sequencing read this file represents. Should be one of: "read1", "read2", "read3", "read4", "index1", "index2" or "single-end, non-indexed".

Read lengthsequence_file.read_length (integer) The length of a sequenced read in this file, in nucleotides. For example "51".

Checksumsequence_file.file_core.checksum (string from file_core) MD5 checksum of the file. For example "e09a986c2e630130b1849d4bf9a94c06".

File nameRequiredsequence_file.file_core.file_name (string from file_core) The name of the file. For example "R1.fastq.gz" or "codebook.json".

File sourcesequence_file.file_core.file_source (string enum from file_core) The source of the file. This is typically an organisation, repository, person or dedicated process. Should be one of: "DCP/2 Analysis", "Contributor", "ArrayExpress", "HCA Release", "GEO", "SCEA", "SCP", "DCP/1 Matrix Service", "LungMAP", "Zenodo" or "Publication".

File formatRequiredsequence_file.file_core.format (string from file_core) The format of the file. For example "fastq.gz" or "tif".

Content description ontology IDsequence_file.file_core.content_description.ontology (string from file_content_ontology) An ontology term identifier in the form prefix:accession. For example "data:3497" or "data:0863".Graph restriction: Subclasses of data:0006, IAO:0000030 from obo:edam or obo:efo.

Content description ontology labelsequence_file.file_core.content_description.ontology_label (string from file_content_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "DNA sequence (raw)" or "Sequence alignment".

Content descriptionRequiredsequence_file.file_core.content_description.text (string from file_content_ontology) General description of the contents of the file. For example "DNA sequence (raw)" or "Sequence alignment".

Accessionsequence_file.provenance.accession (string from provenance) A unique accession for this entity, provided by the broker.

Document IDRequiredsequence_file.provenance.document_id (string from provenance) Identifier for document.

Schema major versionsequence_file.provenance.schema_major_version (integer from provenance) The major version number of the schema. For example "4" or "10".

Schema minor versionsequence_file.provenance.schema_minor_version (integer from provenance) The minor version number of the schema. For example "6" or "15".

Submission dateRequiredsequence_file.provenance.submission_date (string from provenance) When project was first submitted to database.

Submitter IDsequence_file.provenance.submitter_id (string from provenance) ID of individual who first submitted project.

Update datesequence_file.provenance.update_date (string from provenance) When project was last updated.

Updater IDsequence_file.provenance.updater_id (string from provenance) ID of individual who last updated project.