I’ve got an RNA-seq dataset with a large proportion of environmental RNA “contamination”. BLASTing random reads reveals that much of the data comes from bacterial, plant and viral RNA. My target organism only accounts for ~5% of the RNA-seq read data.
I would like to get a more or less (more, if possible) comprehensive overview of what species are found in my sample — bacteria, plants, animals (?), but also viruses. How can I perform this?
I have been unable to find a “standard” way of performing a metagenome screen. BLAST online services all seem to be severely rate limited (certainly unable to handle uploading ~80 M reads). Installing BLAST (or a similar tool) locally is of course not an issue, but I can’t find a comprehensive database that spans all phyla — the best I’ve been able to find are databases, such as NCBI-NR, that are restricted to single phyla or classes, or to bacteria.
Ideally I’d like a workflow that I feed with my RNA-seq data, and get out a list of species with % of reads mapped.