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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___________________________________________________________
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at usegalaxy.org. Please keep all replies on the list by
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