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Question: Retrieve Taxonomic Information
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gravatar for shtorkman
2.8 years ago by
shtorkman • 0
United States
shtorkman • 0 wrote:

Hi Galaxy,

As far as I understand, the Kraken databases are in the process of being switched from the test server to the primary server and that is why there are no database options under Create Kraken. So, I have two questions:

I have Blastn results > 65K gene bank GI and/or Accession numbers. I tired running those in the testgalaxyproject.org and got back Eukarya taxonomy, almost none of the Bacteria. And the amount of taxa returned was about 20 times less of the submitted. So I assume that my dataset is too big for the test version and the wise thing to do, would be to hold on tight and wait =) 

When do you guys estimate to complete the work on Create Kraken function and how are you going to let us know about it? 
I am a bit in a hurry to get that taxonomy )))

Thank you.
galaxy • 711 views
ADD COMMENT • link •
modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by shtorkman • 0
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This data migration will occur near term. I created a ticket to track the progress that can be followed here:

https://github.com/galaxyproject/galaxy/issues/1679

A summary of all reference data updates in progress is here:

https://github.com/galaxyproject/galaxy/issues/1470

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Thank Jen, that will definitely help =) You are, as always,very helpful!

ADD REPLY • link written 2.8 years ago by shtorkman • 0

Hi Jen, I see that right now the Kraken reference data at http://usegalaxy.org #1691 says "Closed". Does it mean that everything is updated? I still can not launch Kreken for taxonomy retrieval. Thank you

ADD REPLY • link modified 2.7 years ago • written 2.8 years ago by shtorkman • 0

Hi Jen, I see that right now the Kraken reference data at http://usegalaxy.org #1691 says "Closed". Does it mean that everything is updated? I still can not launch Kreken for taxonomy retrieval. Thank you

ADD REPLY • link written 2.7 years ago by shtorkman • 0
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