Question: Using entrez or similar to find number of draft or complete genomes are associated with an SRA
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gravatar for nickp60
9 weeks ago by
nickp600
nickp600 wrote:

Hi all, I want to find a straightforward way to determine if a genome in the nuccore database has an associated SRA dataset.

Example: I read this genome announcement. To find out whether there is a SRA dataset associated with it, I need to go to its nuccore entry, then to the bioproject page, and then look at the "project data section" to see if there an included entry in SRA (in this case, there is not).

Is there a way to determine this with Entrez, e-utils, or similar?

entrez next-gen sra ncbi • 206 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by nickp600
1
gravatar for nickp60
9 weeks ago by
nickp600
nickp600 wrote:

Contacted SRA; this was their response:

If a user has a nuccore accession number like “AWUT00000000.1”

They can construct a search like so: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&id=AWUT00000000.1&version=2.0

this will allow them to have access to the BioProject accession number which can be used to search SRA records like so: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term=PRJNA213258

ADD COMMENTlink written 9 weeks ago by nickp600
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