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 <
jen@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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>>
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> --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
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use the Galaxy Development list:
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please use the interface at:
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