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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>
> --
> Jennifer Hillman-Jackson
>
http://galaxyproject.org