A small warning re-the current cloud-Blast+ config.

To properly use the metagenomic tools, if you use the blast+ galaxy tool,
make sure to export in blast.XML, then you'll need a script to parse out
the readID and the Hit_def (as the hit ID).  It appears that the 'Hit_def'
field contains the correct key to the taxonomy database.  Specifically, the
Hit_def field is in the format #_#, where the 'gi' id is the first #.  The
tabular (normal and extended) data does not contain this info.

I noticed this after attempting to use the tabular data, and using a
trimmed col[1] (supposed to be hit seqID), but my results always came back
as a ranked list of the most sequenced genomes in nt.... basically  keying
in randomly.

j

On Wed, Mar 7, 2012 at 4:16 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:

> 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<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/u/aun1/p/windshield-splatter>
> http://main.g2.bx.psu.edu/**library <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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>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/**Support<http://galaxyproject.org/wiki/Support>
>
> ______________________________**_____________________________
> 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
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>  
> http://lists.bx.psu.edu/**listinfo/galaxy-dev<http://lists.bx.psu.edu/listinfo/galaxy-dev>
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___________________________________________________________
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