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What is the recent preference for RNA-seq read deposition perior to publication

Dear Biostars, Hi

Q: I wonder which standard routine and repository is acceptable for present (2018) RNA-seq read deposition perior to publication of a paper?

[NOTE: Date from Illumina Highseq 2000 paired-end De novo non-human vertebrate RNA-seq]

I remember that many years ago, BMC genomics or Plos One preferred RNA-seq read deposition as Sequence Read Archive (SRA) in NCBI as a standard repository. But now it seems that there are something like FAIRsharing, too.

~ Thanks

sra rna-seq repository fairsharing
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updated by i.sudbery i.sudbery • written by Farbod Farbod

I'm not sure they cover the same issue? I would personally still deposit my (raw) data in ENA or SRA.

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written by lieven.sterck lieven.sterck

Deposition to ENA may be relatively less painful than SRA. But in the end be ready to spend some quality time on this (and lose a few hair in the process).

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written by GenoMax GenoMax

I always deposit in GEO (which automatically forwards to SRA/ENA). I've never had any stress with it. Its dull, yes (copying the same info across many boxes), but I can't say a dataset has ever taken me more than a few hours.

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written by i.sudbery i.sudbery

1 answer

GEO (US) or ArrayExpress (Europe), depending on preference. It doesn't really matter which because if you deposit in one, it will be automatically mirrored in the other. Also submission to either results in automatic submission of your data to SRA / ENA.

FAIRsharing is a database of databases, it doesn't accept data itself, but instead will tell you which database will accept your data. GEO and ArrayExpress are both listed under recommended gene expression databases.

The only other major alternatives is dbGaP which takes sequencing data where access must be controlled for privacy reasons (EGA also doesn't this, but I don't know if they take RNAseq data).

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written by i.sudbery i.sudbery

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