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 <j...@bx.psu.edu>:

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


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Jennifer Hillman-Jackson
http://galaxyproject.org



___________________________________________________________
The Galaxy User list should be used for the discussion of
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at usegalaxy.org.  Please keep all replies on the list by
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 http://lists.bx.psu.edu/listinfo/galaxy-dev

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