Bulk RNA seq files

Bulk metadata file : bkrnaseq_metadata_table

• Objective of the file: Contains sample metadata & UMAP coordinates.

• Requirements:

• Named bkrnaseq_metadata_table

• In parquet format

• bk_sample_id as primary key

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
bk_sample_id	str	TRUE	Bulk RNA-seq sample identifier
patient_id	str	TRUE	Patient identifier. Maps to the linked clinical data file. There can be mutliple bk_sample_id for one patient_id.
sample_id	str	FALSE	Maps to the linked sample metadata data file. There is a 1 to 1 relationship between bk_sample_id and sample_id
UMAP_1		FALSE
UMAP_2		FALSE

Patients counts file: bkrnaseq_count_table

• Objective of the file: contains TPM-normalized expressions.

• Requirements:

• Named bkrnaseq_count_table

• In parquet format

• bk_sample_id as primary key

• gene_name fit HGNC ontology

• count_tpm in long format and with “.” decimal separator

• Contains the mandatory columns in the table below

• File columns & description:

Name	Type	Mandatory	Description
bk_sample_id	str	TRUE	Maps to the linked clinical data file. There can be mutliple bk_sample_id for one patient_id.
gene_name	str	TRUE	Gene name fitting HGNC ontology
count_tpm	pl.Float32	TRUE	TPM count value