Hi Jen,

Thank you for getting back to me and for pointing out the live projects, which 
definitely will provide some great resources for me.

Cheers,

Will
On Mar 7, 2012, at 5:50 PM, Jennifer Jackson wrote:

> 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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> 
> -- 
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/Support


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