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The European Nucleotide Archive provides a general guide where all the information you need is available. As it is quite long and complicated. Below is a summary of the different steps one has to follow to put raw FASTQ files into the ENA.
You must upload data files, typically compressed FASTQ files (xxx.fastq.gz), into your private Webin file upload area at EMBL-EBI before you can submit the files through the Webin submission service.
You have several options:
The documentation is well done, please refer to it. If you don’t manage, don’t hesitate to contact us at bibsATparisepigenetics.com.
The easiest is the Interactive submission. See documentation.
There are two Webin Portal services: one for test submissions and another for production (real) submissions. The test service allows you to trial the interface in a consequence-free manner. Any submissions made to the test service will be removed by the following day.
If you don’t have one, you must create a Webin account at https://www.ebi.ac.uk/ena/submit/webin/accountInfo.
Then login to your account at https://www.ebi.ac.uk/ena/submit/webin/login.
The first thing is to register a study, also called project, that will gather different samples and sequencing files. See documentation.
Register Study
.Of note, once the corresponding paper is published, you should add the Pubmed ID to the study.
Then, you can register the samples of the project. Several experiments (or runs) can be attributed to one sample, for instance if you sequence twice the same sample. See documentation.
Register Samples
.Download spreadsheet to register samples
Upload filled spreadsheet to register samples
.
If everything goes fine, you can save accessions at this step.Finally, you can register your reads (FASTQ files) to make the link with the files you have uploaded at the beginning. See documentation.
Submit Reads
.Download spreadsheet template for Read submission
and choose the appropriate template.Upload filled spreadsheet template for Read submission
.On the main page, click on Studies Report
You should see the different studies linked to your Webin account.
Then on Action
, you can select Show runs
.
You should see the experiments you have defined. Then on Action
, you can select Show submitted files
and see the names of the FASTQ files you have uploaded.
To go quickly to the run, you can click on Run Files Report
directly from the main page.
In the column Archive status
, the new files should have File submitted
. It will then turn to File archived
.
Data release is controlled from the level of study objects. When a study is made public, all samples, experiments, runs and analyses associated with it are also made public.
Follow all the steps except Register Study
. And put the correct study name in the spreadsheet for Read submission.
Right after submission the data is private. If the study is public
, the new samples will turn public within a few days (??).
BiBs
2023 parisepigenetics
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