Question: Sra Data: Getting Rna-Seq /Ncrna Experiments Ids For A Taxon
2
gravatar for Darked89
8.2 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

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

sra small rna • 2.1k views
ADD COMMENTlink modified 8.2 years ago by Hamish3.1k • written 8.2 years ago by Darked894.2k
1

This is DB used/downloaded by SRAdb R package mentioned in this post: http://biostar.stackexchange.com/questions/1837/searching-ncbis-short-read-archive Instead having R in which I will type SQL commands I used SQLite directly.

ADD REPLYlink written 8.2 years ago by Darked894.2k

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

ADD REPLYlink written 8.2 years ago by Pierre Lindenbaum120k
1
gravatar for Hamish
7.3 years ago by
Hamish3.1k
UK
Hamish3.1k wrote:

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.

ADD COMMENTlink written 7.3 years ago by Hamish3.1k
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