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emo-bon / sequencing-data

The files controlling and describing the sequencing metadata
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Changes conflicting in pull request #8

Open cpavloud opened 2 months ago

cpavloud commented 2 months ago

I propose these changes to the run-information-batch-001.csv, run-information-batch-002.csv, run-information-batch-001_column-descriptions.csv and run-information-batch-002_column-descriptions.csv:

  1. The proper name of the parameter in the https://github.com/emo-bon/sequencing-data/blob/main/shipment/batch-002/run-information-batch-002_column-descriptions.csv is "dna_quant", not "dna_quantity_after_extraction"
  2. The proper name of the parameter in the https://github.com/emo-bon/sequencing-data/blob/main/shipment/batch-001/run-information-batch-001_column-descriptions.csv is "dna_quant", not "dna_quantity_after_extraction"
  3. "paired" should be "PAIRED" (this is the appropriate value for the submission to ENA
  4. The metadata full term "analysis" was repeated twice. Actually, what is term 20 is the "library_source" field that ENA requires for submission of reads.
  5. "seq_meth" is actually the "instrument_model" in the ENA reads submission
  6. Extra terms should be added: extraction_blank,pcr_blank_1,pcr_blank_2 Those terms should be defined as: 31,extraction_blank,correspoding extraction blank sequencing reads filename,Filename given by the sequencing centre to the sequencing reads produced by the extraction blank included in the same sequencing run as the sample,text,CDX_ABMLOSTA_1_1_HGVH5DRX3.UDI363,Sequencing,Genoscope; Ioulia Santi,Optional (O),, 32,pcr_blank_1,correspoding 1st pcr blank sequencing reads filename,Filename given by the sequencing centre to the sequencing reads produced by the 1st PCR sequencing blank included in the same sequencing run as the sample,text,CEB_DCXOSTA_1_1_HGVH5DRX3.UDI363,Sequencing,Genoscope; Ioulia Santi,Optional (O),, 33,pcr_blank_2,correspoding 2nd pcr blank sequencing reads filename,Filename given by the sequencing centre to the sequencing reads produced by the 2nd PCR sequencing blank included in the same sequencing run as the sample,text,CEB_DCYOSTA_1_1_HGVH5DRX3.UDI364,Sequencing,Genoscope; Ioulia Santi,Optional (O),,

@melinalou