Hello,
The publication and supplemental material for the metagenomics data and
tools available in Galaxy described in:
Windshield splatter analysis with the Galaxy metagenomic pipeline
is available on the main public Galaxy instance at:
Shared Data -> Shared Published Pages -> Windshield Splat
blem.
Thanks
Vincent
From: John Major [john.e.major...@gmail.com]
Sent: Monday, March 12, 2012 11:28 AM
To: Jennifer Jackson
Cc: Montoya, Vincent; galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Metagenomics
A small warning re-the current cloud-Blast+ config.
Major [john.e.major...@gmail.com]
Sent: Monday, March 12, 2012 11:28 AM
To: Jennifer Jackson
Cc: Montoya, Vincent; galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Metagenomics
A small warning re-the current cloud-Blast+ config.
To properly use the metagenomic tools, if you use the blast+ gala
Hi Scott,
There isn't a specific tool to do this filtering in one step, but tools
similar to those used in the in the Windshield analysis can be used again.
Starting with " Parse blast XML output" results (this tool is on the
Galaxy main server), calculate percent coverage (of the query) and
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
On Mon, Mar 12, 2012 at 6:28 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
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 corre
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 Nekrutenk
Vincent
Great question!!! And a follow up for me, is how to purge the conserved
sequences. Presently the current data set I have from "Fetch" is likely
to be 99% composed of incorrect taxon just because of conserved
sequence. So, how do you select just unique sequences (ie those that do
not
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
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