description of "Find diagnostic hits"
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
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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
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William Hsiao