Question: What is the difference between GEO and SRA ncbi databases?
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gravatar for matija.sosic
5.4 years ago by
matija.sosic80
Croatia/Zagreb/Faculty of Electronical Engineering and Computing
matija.sosic80 wrote:

I found that GEO holds "processed sequence data files", while SRA holds "raw sequence data files". In which way processed?

I am interested in rna-seq bacterial data, is GEO right resource for me?

ncbi sra geo • 7.6k views
ADD COMMENTlink modified 5.4 years ago by Chris Fields2.1k • written 5.4 years ago by matija.sosic80
9
gravatar for Chris Fields
5.4 years ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k wrote:

Depends on your needs.  GEO contains data relevant to a particular experiment and in most cases I believe represent processed data (e.g. have been run through one or more analysis steps, such as trimming, alignment to a reference, R/BioC, etc).  The example RNA-Seq from GEO is illustrative:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25180

If you check under the BioSamples you'll find a Cufflinks file, a SAM file, BEDGRAPH, etc.  These would all be bound to a specific assembly version and whatever comes along with that (annotation, etc).

SRA however contains raw sequence data for an experiment, if you want to download and re-analyze the data on your own.  They are generally all tied together via a common BioProject ID.

EDIT: In that last sentence, by 'they' I mean any data relevant to the BioProject (BioSamples, SRA, assemblies, etc).

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Chris Fields2.1k
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