Raw Data Requirement for RNA-Seq paper submission

Question

[babalyigit]

Hello,

My PhD thesis is mostly related about RNA-Seq analysis by using public available datasets form GEO. I am using Galaxy Platform to perform my raw sequence analysis. I do not have computational power and high storage capacity. I am saving all of my count matrix resulted from FeatureCounts , but could not save trimmed reads, BAM files etc. to my computer. Additionally, Galaxy Platform gives only 250GB storage. Therefore, I could not save these files into Galaxy history too. When it's time to submit my results to any journal which have peer-review processes, will these files (trimmed reads, BAM/SAM files) be required for submission or during peer-review processes?

Thanks

[piyushjo]

You just need to upload the fastq files and a processed counts/rpkm file.

Answer 1

[GenoMax]

My PhD thesis is mostly related about RNA-Seq analysis by using public available datasets form GEO.

If these data are already in GEO/SRA then you can't resubmit again.

I am not sure what conclusions you are drawing but for raw data you can point people to relevant Accession numbers. Journals would not need aligned data files for review. You can try one of the data repositories mentioned in this blog for rest of derived data e.g. count tables etc.

Answer 2

[lieven.sterck]

They are indeed not required though some of them could be recommended (BAM files for instance).

The bare minimum you should deposit to be somewhat compliant with FAIR are the raw input reads and ideally also the count matrix (or matrices).

EDIT: I did not read the question careful enough. As this is public data you can indeed not (and don't have to obviously) submit this data as it was raw data. Follow @genomax answer here.