Japanese Genotype-phenotype Archive
JGA submission steps
Data submission application to NBDC
Submit a data submission application in the NBDC application system. Create a data submitter group before application. After the application is apprived by NBDC, an upload directory will be created in the JGA server.
For application, a D-way account is required. Please obtain a D-way account before application.
After creating a D-way account, it takes about 10 minutes for the D-way account becomes active in the NBDC application system.
This page describes how to submit data to JGA.
Data submitter group
Create a data submitter group before application. In the example group “subgrp1”, a researcher (account_b) who applies application and submits data is a group owner and a PI (account_c) is a member.
In the NBDC application system, an account who actually submits an application will automatically become an applicant. If there are submitters other than PI and applicant, include all submitters as members. Emails regarding the submission are sent to members.
Start the data submission application process and select the data submitter group.
Data submission application approval
After the application is approved by NBDC, a JGA submission ID (for example, JSUB000353) is issued and a corresponding directory for data upload is created in the JGA server.
A JGA submission directory is created in “/controlled-access/submission/jga/” of the JGA file server (jga-gw.ddbj.nig.ac.jp), upload metadata and data files to this directory by sftp. In this example, the upload directory is “/controlled-access/submission/jga/JSUB000353/”.
Create metadata excel
Enter metadata in the excel
Download the excel for metadata description below and enter metadata in English. Regarding metadata, see this page.
last updated: 2020-09-26
Data files to be uploaded to JGA should not have spaces in their filenames.
All datasets in a JGA submission are distributed at the same time. Do NOT include datasets to be distributed at different time in a submission.
Example metadata
Upload excel
To upload files to the JGA server by sftp, you need to register a center name and a public key to your D-way account. The ssh login is blocked in the JGA server.
In the JGA submission directory in “/controlled-access/submission/jga/” in JGA file server (jga-gw.ddbj.nig.ac.jp), upload the excel to this directory by sftp specifying the port number 443 with P option. The sftp uses public/private key authentication, specify a private key registered to your D-way account for authentication.
Example
- account ID: account_b
- JGA Submission ID: JSUB000353
$ sftp -i private-key-for-auth -P 443 account_b@jga-gw.ddbj.nig.ac.jp
$ cd controlled-access/submission/jga/JSUB000353
$ put JSUB000353_metadata.xlsx
-i: specify the private key for authentication -P: specify the port number 443
Data files uploading
Data file format
The JGA submission system discriminates archive and compression formats by the extension of the filenames.
- The extensions, zip, tar, tar.gz, tgz, tar.bz2, tbz2, gz and bz2 are treated as archived and compressed in standard formats. Files whose extensions and formats are different will cause errors in the file processing.
- Do NOT compress bam files.
- Do NOT archive files compressed by gz and bzip. Instead, archive compressed files by tar.gz.
File formats for submission
Submit individual-level next-generation sequencing data such as fastq and bam files to Data. And submit microarray data, variant analysis data and documents such as questionnaires to Analysis.
For reproducibility, it is important to submit processed data from which conclusion of associated paper is derived. Please submit processed data files such as VCF to Analysis.
Upload data files
Upload data files to the upload directory by sftp.
Example
- Account ID: account_b
- JGA Submission ID: JSUB000353
$ sftp -i private-key-for-auth -P 443 account_b@jga-gw.ddbj.nig.ac.jp
$ cd controlled-access/submission/jga/JSUB000353
$ put wgs1.fastq
-i: specify the private key for authentication -P: specify the port number 443
Upload all files with “fastq” in the extensions.
$ mput *.fastq
Submission of metadata and data files
The JGA curator reviews your metadata and data files. After reviewing process, the curator creates XML files from the metadata excel and submit them.
After the metadata and data files pass the validation, accession numbers will be issued.