Question: What is the difference between SRR, DRR, ERR ?
1
gravatar for Helen
7 weeks ago by
Helen30
Helen30 wrote:

Hello,

I downloaded a file called "SRA_Accessions.tab" from the SRA ftp server which contains various data for each SRA run on the SRA database, including its associated GEO accession code.

I'd to know if it's enough to use the SRR codes or should I use the DRR and ERR codes too? What is the difference between them ? Except that they are in different data bases..

thx

rna-seq sra • 205 views
ADD COMMENTlink modified 7 weeks ago by Malka20 • written 7 weeks ago by Helen30
2
gravatar for genomax
7 weeks ago by
genomax69k
United States
genomax69k wrote:

The first letter of the accession prefix shows which International Nucleotide Sequence Database Collaboration (INSDC) archive the data originated from (S =NCBI-SRA, E = EMBL-SRA, D = DDBJ-SRA:

Data is synced nightly between the databases (though it may take a few additional days for the data to fully propagate to other two databases).

Take a look at this link for more.

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by genomax69k

Thank you you mean that it's the same ? specific run accession will be found in the three databases?

ADD REPLYlink written 7 weeks ago by Helen30
2
gravatar for Malka
7 weeks ago by
Malka20
The Hebrew University, Jerusalem, Israel
Malka20 wrote:

When a sample is uploaded to one of the 3 SRA databases, it is assigned a unique identifier depending on the database it is submitted to (see below). The databases are regularly synchronised, and the run is therefore found on all 3 databases, with the same accession code on all of them.

If you choose to use only SRR accession codes, you would be limiting yourself to runs which were originally submitted to NCBI's SRA database and not EBI's or DDBJ's databases.

Explanation About SRA Accession Codes

SRA = Sequence Read Archive

Accession code format: aRbx (Examples: SRR#, SRX#, ERR#, DRR#, etc.) Where:

First letter (represented by 'a' above) Represents the source database to which the sample was originally uploaded, before being synchronised with the other 2 databases:

S – NCBI’s SRA database

E – EBI’s database

D – DDBJ database

Second Letter

Always the letter R

Third letter (represented by 'b' above) Type of data represented:

R – Run

X – Experiment

S – Sample

P – Project / study

x - unique accession code

Or if this is easier:

"There are four hierarchical levels of SRA entities and their accessions:

  1. STUDY with accessions in the form of SRP#, ERP#, or DRP#

  2. SAMPLE with accessions in the form of SRS#, ERS#, or DRS#

  3. EXPERIMENT with accessions in the form of SRX#, ERX#, or DRX#

  4. RUN with accessions in the form of SRR#, ERR#, or DRR#

The first letter in the accession makes a notation of the source database - SRA, EBI, or DDBJ correspondingly.

Examples of searches by accession:

Find one specific study: SRP006081

Find studies with consecutive accessions using wild card: SRP00608*

Find two specific studies: SRP006081 OR SRP006083"

Source for above quote: NCBI's SRA search help

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Malka20
2

P – Publication

Actually, P is for Project here. There can be an SRP study that has not been published at all.

ADD REPLYlink written 7 weeks ago by vkkodali1.1k

You are right. I mistakenly wrote 'publication' instead of 'project'. I corrected it. (Couldn't reply yesterday because I don't yet have enough points...)

ADD REPLYlink written 7 weeks ago by Malka20
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