[BioC] SRAdb: is the database missing some entries?

[Sean Davis]

On Sat, Jun 9, 2012 at 8:20 PM, Ben Woodcroft <donttrustben at gmail.com> wrote:
> Hi,
>
> Firstly thanks to the creators of this very useful package.
>
> I've come across SRA identifiers that don't appear to be in the database (a
> minority, but still). Here's a few:
>
> SRA036600
> DRX001436
> SRA049463
> ERA062401
> ERA062401
>
> For example:
>> library(SRAdb)
>> sra_con = dbConnect(SQLite(),'SRAmetadb.sqlite')
>> sraConvert(c('SRA036600'), sra_con= sra_con)
> [1] submission study      sample     experiment run
> <0 rows> (or 0-length row.names)
>
> However this isn't a bogus accession because I can see it on the NCBI SRA
> website.
>
> I could be wrong but I don't think it is as simple as the metadata being
> out of date because the submission dates are often relatively old
> (SRA036600 was 2011-05-13) and there's metadata from more recent SRA
> submissions in the SRAdb).

Thanks, Ben.

We'll look into it.  Sorry for the inconvenience.

Sean