Hi Will,

An short description of what the Metagenomics tools do is on each of the tool forms. One bit that many be confusing is that what is often called the "Fetch Taxonomic Ranks" tool on these forms has been renamed to be the "Fetch taxonomic representation" tool.


In short, the "Find diagnostic hits" tool will pull out sequences that have hits with an assignment to the user specified taxonomic rank(s) set on the tool form. At this stage in the analysis, hits would have already been filtered.

Rather than explaining these methods in an email, it would likely be more helpful if you were to review the associated paper and supplemental data. This includes a tutorial that demonstrates step-by-step the exact methods used for the published metagenomics analysis project using these exact tools. All of this is available in Galaxy as a live project that can be imported and experimented with.
Supplemental home page:
http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter
Raw data:
http://main.g2.bx.psu.edu/library -> see "Windshield splatter"

Hopefully this helps!

Best,

Jen
Galaxy project

On 2/15/12 5:08 PM, William Hsiao wrote:
Hi,

Is there a more detailed explanation on what "Find Diagnostic hits" module in 
Metagenomic analysis does?  Does it take all the hits above user specified cutoffs to one 
query and return the taxon name if and only if all the hits have the same taxon (my 
understanding)? Or, does it look at the top few hits or???  Thanks for providing some 
clarification on the method.

Cheers,

Will
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