Hello,

I'm trying to collect RNA-seq datasets for co-expression network analysis. I've been using both SRAdb and GEOmetadb to search and have experienced limited success with both, for different reasons.

Using SRAdb, I was able to isolate all RNA-seq experiments (from a column describing "library_strategy"). However, based on this question and answer it seems like the Sequence Read Archive provides raw data, and I would really prefer to find datasets that have already been aligned and processed for memory reasons.

The issue with GEOmetadb is that there doesn't seem to be a column that includes "RNA-seq" as a category. I've tried searching using "Illumina" as the manufacturer, but this does not exclusively select RNA-seq datasets. Looking for entries whose description mentions "RNA-seq" yields a suspiciously few number of entries.

Has anybody else tried to use GEOmetadb to select multiple RNA-seq datasets? If so, how did you do this? Am I going to have to bite the bullet and just use the online GEO gui?

Thanks,
Maureen