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Data submission

General instructions to submit data in GnpIS.

 

Project data

This step is only required when your data concern a project, contacts, institutions or publication that are not yet in our database. To know if your project, contacts, institutions or publication is already stored in GnpIS, consult the "static data" tab that is embedded in our excel metadata submission files.

Submission of project, contacts, institutions and publications

Use the excel file to submit your data:

 

Genotyping and SNP discovery submissions

Two files must be prepared for each submission: the genotyping raw data file and a metadata file describing the experiment, the markers and the plant material. 

  1. Prepare your raw data matrix file: VCF format or a marker*plant matrix as for example Genome Studio matrix format are accepted. For the matrix format, we accept either accessions in columns and markers in lines or the reverse. 
  2. Prepare your metadata files. Please use the dedicated   depending which format you choose for the genotyping data file:

      3. Submit you data: prepare an archive containing the two files (excel metadata and matrix or VCF genotyping files)

  • if the archive is not too big (< 2Go; please compress if necessary): use the submission interface to upload it..
  • if the raw data file is > 2Go, please contact us (at urgi-support[[@]]inrae.fr).

 

CNV (Copy Number Variations) discovery submissions

Two files must be prepared for each submission: the CNV calling analysis output and a metadata file describing the experiment, the markers and the plant material. 

  1. Prepare your CNV calling analysis output file: VCF format is recommended but other standard formats (ie GFF3, GenomeStudio) are accepted.
  2. Prepare your metadata files. Please use the following template: CNV analysis Metadata.xlsx
  3. Submit your data: prepare an archive containing the two files:
    • if the archive is not too big (< 2Go; please compress if necessary): use the submission interface to upload it.
    • if the raw data file is > 2Go, please contact us (at urgi-support[[@]]inrae.fr).
Update: 24 Aug 2020
Creation date: 07 Jun 2010