I used the NCBI BLAST+ blastn in Galaxy and get a return of approximately the same number of hits as my reads (approx 50,000). However when i use the Fetch Taxonomic Representation tool, I only get back some of the hits (10% or so), not in the same order, and with the correct annotation. I do have to use the Convert tool on the megablast result file because the FTR tool will not recognize the gi numbers with the pipes in the names (so I change the pipes to tabs). Manually checking the file, this appears to not introduce any errors. Help is appreciated! Thanks!
The Fetch Taxonomic rep tool at http://usegalaxy.org has been pre-loaded with annotation that is a match for the Genbank databases available in the Megablast tool.
If you wish to use this function successfully with other databases, the tool can be installed and used in a local. If that is where you are using it already (a local or cloud would be needed for BLAST+), then double check how the data the tool is accessing is populated. It could be missing divisions or it is outdated or a mismatch for the blast databases.
Thanks, Jen, Galaxy team