Subbmission Data

Question

[GiV17]

Dear all,

I have a doubt.

If I submit a work of rna-seq or any other sequencing data to any scientific journal, am I OBLIGED TO SUBMIT even the fastq files or are ok even the raw count matrix?

Thanks

[GenoMax]

In order for others to be able to reproduce your results you should submit original fastq data. Some journals may require it as a condition of publication. If it is human/patient data then you can submit it via controlled access database like dbGAP.

[GiV17]

Sorry, But is it obligatory? My question is this.

[GenoMax]

AFAIK sequence files are required for submission to GEO/SRA.

[GiV17]

What? I did not understand

[GenoMax]

GEO/SRA are standard repositories for sequence data submission. Here is the relevant section from GEO: https://www.ncbi.nlm.nih.gov/geo/info/seq.html#raw

You can check that entire page to get more information.

[seidel]

Only the journal knows the answer to this. In general, journals will require submission to a repository, but each journal sets their own rules for publication requirements, and the editor will enforce them.

Answer 1

[ATpoint]

Yes, it is obligatory. If there is a journal that indeed accepts publication without deposition of raw (fastq) data then imo it disqualifies from any scientific integrity.

[GiV17]

Thanks, but, do you have a reference to say this? Is there a reference guide? So what about those jobs where I only saw the rawcount and not the raw fastq files?

[ATpoint]

Journals usually have guidelines on that. As said, all non-trash/non-predatory journals with some basic integrity typically require it. Examples:

https://www.embopress.org/sourcedata#5

https://ashpublications.org/blood/pages/editorial_policies -- see section ' What is the point? Data sharing, distribution of reagents, and compound structure disclosure'.

Don't you have the raw data? No raw data means that your work is not reproducible. That's not a badge you want to have on your resumée, is it?

[GiV17]

I have the raw data, fastq files, but I didn’t want to submit them already, for further analysis I’m conducting, but I wanted to publish a first work. is it possible?

[GenoMax]

Probably not. Journals will require an accession number from SRA and for that you will need to submit the data.

You can ask for the data to be embargoed (kept private) for a certain period (generally until the paper is published) but there is probably an outer limit. It would again depend on the policy of the journal where you are hoping to publish, which may require the data to be available once the paper is published. Raw data may also need to be made available to reviewers (even though it may not be public at that point).

[seidel]

GEO allows you to keep your data private for up to three years, AND has a mechanism where you can share it with reviewers without it being available to the public. However, once you quote the accession number in a publication, GEO will make it public if you haven't already released it.