riboPicker: standalone ref_id issue

[aarong...@gmail.com]

Hello

I have been using the standalone version of riboPicker (and I love it). But I'm having one problem. I've been using the "-keep_tmp_files" flag which gives me a .tsv file with a reference id for each of the sequences identified as rRNA. However, I can't seem to find what organism the id's belong to.

For example:
ncbibact2012011723S_546
slr108_1073
gg20110531_740188

when I google these names I get no results. And when I go to specific databases like ncbi and search for the names I still come up with nothing.

Could you point me to a resource I can use to "de-code" the reference ids?

Thanks

Aaron

[Robert Schmieder]

This seems to be somewhat hidden in the FAQ's (http://ribopicker.sourceforge.net/faq.html). Under "Is there a standalone version of the program", we list the FTP and HTTP access to the databases. The same location (e.g. http://edwards.sdsu.edu/ribopicker/rrnadb/) contains the taxonomy data in a tab separated file that maps the riboPicker ID to the taxonomy.

For example:

	ncbibact20120117.tar.gz	24-Feb-2012 11:02	12M
	ncbibact20120117taxon.tar.gz	24-Feb-2012 11:05	63K

[aarong...@gmail.com]

Awesome! Thanks Rob!

[helenhi...@gmail.com]

Hello,

I've also been using the taxon files to get the reference ids. Mostly it is great but I think there is a problem with one of the files. Every line in ncbibact201201175S has the ref_id 'ncbibact201201175S_1' so I don't think it is possible to tell the NCBI accession for this database. Unless I am making a mistake/missing something?

Thanks,
Helen