Experiment Data

Data Submission

Access the Data Submission and Management module

Access https://platform.rd-connect.eu/datamanagement/#/

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Left side-bar (1) - Side-bar fixed in all experiment submission and management steps - provides direct access to different experiment submission and management steps. Bottom menus (2) - Menus containing access to submit and manage your experiments.

The process to submit your experiments is the following (and in this order):
  1. Provide experiment metadata

  2. Provide file metadata

  3. Upload sequencing files through RedIris server

Please mind that:
  • Steps 1 and 2 are performed following the “Submit Data” section.

  • Step 3 is performed outside the RD-Connect GPAP website.

Important

Be aware you will need the Phenostore IDs to begin the data submission process.

Provide experiment metadata

In the Experiment Submission Site enter the Submit Data section in the bottom menu. You will see 2 sections, one to submit an Experiment metadata and one to submit File metadata. Enter the “Submit Experiments” section.

You will enter the site to provide the experiment metadata.

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There are 2 methods to submit the experiment metadata:
  1. Individual upload using the website’s form (one row per experiment)

  2. Bulk upload by using a .tsv file

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Once the information appears in the form, click “Validate” to check for possible errors. If no errors appear, click on “Submit” to submit your data.

Important

This step will generate new “GPAP Experiment IDs” for your experiments.

A new page will appear with a summary for your submission.

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Use the button “Download as csv” to download a file with a summary of your submission, including the newly generated Experiment IDs. Use the button “Go to Submit File(s)” to submit files metadata.

Provide file metadata

In the Experiment Submission Site enter the Submit Data section in the bottom menu. You will see 2 sections, one to submit an Experiment metadata and one to submit file metadata. Enter the “Submit Files Metadata” section.

There are 2 methods to submit the file metadata:
  1. Individual upload using the website’s form (one row per file)

  2. Bulk upload by using a .tsv file

_images/submit_options_files.png

Once the information appears in the form, click “Validate” to check for possible errors. If no errors appear, click on “Submit” to submit your data.

Important

Be aware this step is to upload file metadata, not to upload the sequencing files, which is done in Step-3 “Upload Sequencing Files”.

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A new page will appear with a summary of the submission.

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Use the button “Download as csv” to download a file with a summary of your submission, including the newly generated Experiment IDs.

Upload sequencing files through RedIris server

After performing Step-2 “Upload File Metadata” you will immediately receive an email titled “Submission of Sample file/s” with a summary of your submission.

In the next 24 hours you will receive another email titled “Red Iris Account Created”. This email will contain:
  • Login credentials to use RedIris server (https://fileshare.rediris.es).

  • Instructions to upload sequencing files through Web.

  • Instructions to upload sequencing files through Command Line.

After you follow these instructions and the files are uploaded, we will download them from RedIris and begin the data processing.

Data Management

In the “Manage Data” section you will be able to manage:
  • Experiment metadata

  • File metadata

  • Statistics on Data Access

  • Experiment Analysis Status

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Experiment Metadata

In this section you can:
  • See the experiments you have submitted through Step-1 “Provide Experiment Metadata”.

  • Download data using the “Download Table to CSV” button.

  • Access information of each experiment by clicking in each Experiment ID.

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File Metadata

In this section you can:
  • See the files you have submitted through Step-2 “Provide File Metadata”.

  • Download data using the “Download Table to CSV” button.

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Statistics on Data Access

In this section you can:
  • See which experiments have been accessed by other users “Individually” or by the “Search across all” option.

  • Download data using the “Download Table to CSV” button.

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Experiment Analysis Status

In this section you can:
  • See the tagged variants for your experiments.

  • Download data using the “Download Table to CSV” button.

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