Hi Vincent, Scott,
Filtering raw hits is an important part of a metagenomics analysis
pipeline. Please see the methods described in the published metagenomics
analysis paper associated with this tool set:
Koskovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor
J, and Nekrutenko A. "Windshield splatter analysis with the Galaxy
metagenomic pipeline". Genome Research. 2009 Nov; 19(11):2144-53.
http://www.ncbi.nlm.nih.gov/pubmed/19819906
Live supplemental data that can be imported and experimented with is
available on the public instance, including raw data, working histories,
and a tutorial that demonstrates step-by-step the exact methods used in
the publication:
http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter
http://main.g2.bx.psu.edu/library -> see "Windshield splatter"
Not all tools are available on the public main server, but a local or
cloud instance could be used with wrapped tools from the Distribution or
Tool Shed, as necessary. For example, BLAST is not available on the
public instance, but is included in the distribution for use in local or
cloud instances. http://getgalaxy.org
Hopefully you will both find this helpful,
Jen
Galaxy project
On 2/29/12 5:32 PM, Montoya, Vincent wrote:
Hello
I am a relatively new user on Galaxy and I had a question regarding "Fetching
Taxonomic Information". It is great that I can retrieve all of the hits for each
sequence, but I cannot seem to find an option to also provide how accurate of a match it
is to the given taxon. For instance, a percentage match. I can access this information
in the original file and programmatically retrieve it but, it would be nice if it came in
one package so that I can avoide those false hits that have a low percentage match. Can
you please provide me with instructions on how to best to retrieve this information
(hopefully in a single file)?
Thank you
Vincent
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___________________________________________________________
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:
http://lists.bx.psu.edu/
