Hi David: thank you for this excellent example! Right now I am trying to make use of the local SRAdb without much online querying, if not working, that shall be a next step.
Is there a way to filter out files by a taxon and a tissue in SRAdb?
Hi guys:
I wonder how to get links for FASTQ files using Bioconductor SRAdb package for specific taxons and tissues? Currently I am trying to get through by using JOINs and fulltext searches with LIKE, but it is so slow to figure it out..., maybe someone already has solved that?
Thanks!
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I don't know about SRAdb or what metadata that database contains, but you can use entrez to search SRA with the normal limits (including organism)
library(rentrez)
entrez_search(db="sra", term="Tetrahymena[ORGN]")
# Entrez search result with 113 hits (object contains 20 IDs and no cookie)
It looks like tissue isn't a specified term for tissue
> entrez_db_searchable("sra")
Searchable fields for database 'sra'
ALL All terms from all searchable fields
UID Unique number assigned to publication
FILT Limits the records
ACCN Accession number of sequence
TITL Words in definition line
PROP Classification by source qualifiers and molecule type
WORD Free text associated with record
ORGN Scientific and common names of organism, and all higher levels of taxonomy
AUTH Author(s) of publication
PDAT Date sequence added to GenBank
MDAT Date of last update
GPRJ BioProject
BSPL BioSample
But you could search for biosamples that match you query, then find links to SRA?
entrez_search(db="biosample", term="Mouse[ORGN] AND Tissue Liver[Attribute]")
Entrez search result with 2934 hits (object contains 20 IDs and no cookie)
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