Dear GALAXY and Jennifer
Although the windshield analysis papers were good starters, They do not
address conversed sequence purging or how to get at this information. If
anyone has an automated approach I'd be interested . [Discard sequences
from blast that have more then 4 hit >99%]
Scott
Scott Tighe
Advanced Genome Technology Lab
Vermont Cancer Center at the University of Vermont
149 Beaumont Avenue
Health Science Research Bd RM 305
Burlington Vermont USA 05405
lab 802-656-AGTC (2482)
cell 802-999-6666
On 3/12/2012 2:28 PM, John Major wrote:
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
<mailto: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
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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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
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on the list by
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To manage your subscriptions to this and other Galaxy lists,
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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:
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
___________________________________________________________
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:
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To manage your subscriptions to this and other Galaxy lists,
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