Dear Galaxy
When running HiSeq shot metagenomics sample from the environment
against megablast and taxonomic representation, How do I filter/remove
all the 16s and other conserved sequences.
The problem if blasting a single organism that has a fraction of
conserved sequence, the results will align with E.coli 10,000 times
more then the possible target organism. This data would be wrong and
misleading. For example a 100mg sample that was negative for e coli
using MUG test, give thousands of hits with galaxy.
1) Is there a "filter conserved sequences" setting?
2) Is there a "remove model organisms" setting?
Scott Tighe
--
Core Laboratory Research Staff
Advanced Genome Technologies Core
Deep Sequencing (MPS) Facility
Vermont Cancer Center
149 Beaumont Ave
University of Vermont HSRF 303
Burlington Vermont USA 05045
802-656-AGTC
802-999-6666 (cell)
Quoting Jennifer Jackson <[email protected]>:
Hello Elwood,
Are you still having connection issues today? Or is this resolved?
Best,
Jen
Galaxy team
On 9/13/13 11:36 AM, Elwood Linney wrote:
A message sent earlier this week by me indicated that I could not
connect to Galaxy via Fetch to download data.
A reply indicated a glitch was fixed.
I then could connect with Fetch and I tried to transfer 4 x 16gb
files and the connection disconnected about 4 times.
Now, once again, I cannot connect with Galaxy online to transfer data.
Is this a problem that can be solved-either at my end or at Galaxy?
Elwood Linney
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
