Sra Data: Getting Rna-Seq /Ncrna Experiments Ids For A Taxon

Question

[Darked89]

I got SQLite database containing SRA metadata from:

http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz

My problem: many tables with many columns with often non obvious content.

Columns from experiment table:
design_description TEXT,
library_name TEXT,
library_strategy TEXT,
library_source TEXT,
library_selection TEXT,
library_layout TEXT,
library_construction_protocol TEXT,

can have empty values, contain "OTHER". The most obvious columns (librarysource and librarystrategy) do not contain anything LIKE "%RNA%" in it save for "VIRAL RNA".

Any ideas how to get RNA-Seq small/ncRNA experiments/runs for a given species?

edit: +VIRAL RNA

[Darked89]

This is DB used/downloaded by SRAdb R package mentioned in this post: Searching Ncbi'S Short Read Archive

Instead having R in which I will type SQL commands I used SQLite directly.

[Pierre Lindenbaum]

what is that database ? How did you get this URL ?

Answer 1

[Hamish]

Ah that database appears to be specifically created for the SRAdb BioConductor package. Since it is unclear from the description how often it is updated and which information from the SRA it contains, I suspect your best course of action is to contact the BioConductor folks (via their mailing lists). It may be that the data you require is not currently in the database and they need to add it.