HCA Data Portal

Sequence file

A file of read sequences generated by a sequencing experiment.

View JSON source: sequence_filedoneShow required fields only


INSDC run accessionsequence_file.insdc_run_accessionscopy (array) An International Nucleotide Sequence Database Collaboration (INSDC) run accession. For example "SRR0000000".
Lane indexsequence_file.lane_indexcopy (integer) The lane that this file was sequenced from. For example "1".
Library preparation IDsequence_file.library_prep_idcopy (string) A unique ID for the library preparation. For example "tech_rep_group_001".
Read indexRequiredsequence_file.read_indexcopy (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_lengthcopy (integer) The length of a sequenced read in this file, in nucleotides. For example "51".
Sequence file>File coreRequired (file_core object) Core file-level information.
Checksumsequence_file.file_core.checksumcopy (string from file_core) MD5 checksum of the file. For example "e09a986c2e630130b1849d4bf9a94c06".
File nameRequiredsequence_file.file_core.file_namecopy (string from file_core) The name of the file. For example "R1.fastq.gz" or "codebook.json".
File sourcesequence_file.file_core.file_sourcecopy (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", "Publication" or "DCP/2 Ingest".
File formatRequiredsequence_file.file_core.formatcopy (string from file_core) The format of the file. For example "fastq.gz" or "tif".
Sequence file>File core>Content description (file_content_ontology array) General description of the contents of the file.
Content description ontology IDsequence_file.file_core.content_description.ontologycopy (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_labelcopy (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.textcopy (string from file_content_ontology) General description of the contents of the file. For example "DNA sequence (raw)" or "Sequence alignment".
Sequence file>provenance (provenance object) Provenance information provided by the system.
Accessionsequence_file.provenance.accessioncopy (string from provenance) A unique accession for this entity, provided by the broker.
Document IDRequiredsequence_file.provenance.document_idcopy (string from provenance) Identifier for document.
Schema major versionsequence_file.provenance.schema_major_versioncopy (integer from provenance) The major version number of the schema. For example "4" or "10".
Schema minor versionsequence_file.provenance.schema_minor_versioncopy (integer from provenance) The minor version number of the schema. For example "6" or "15".
Submission dateRequiredsequence_file.provenance.submission_datecopy (string from provenance) When project was first submitted to database.
Submitter IDsequence_file.provenance.submitter_idcopy (string from provenance) ID of individual who first submitted project.
Update datesequence_file.provenance.update_datecopy (string from provenance) When project was last updated.
Updater IDsequence_file.provenance.updater_idcopy (string from provenance) ID of individual who last updated project.