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Question: fetch taxonomic representation question
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gravatar for ghrose
4.5 years ago by
ghrose • 0
United States
ghrose • 0 wrote:

Dear Galaxy,

I am getting strange results back when using Fetch Taxonomic Representation.

When I megablast my sequence( below) against nt, on usegalaxy.org, I get back 250 results.

>solo
TTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGA

Then using "Fetch Taxonomic Representation" I get an empty file.

I have checked some of the GIs at NCBI and they come back with a hit.

Am I using doing something wrong?

Thanks

George

 
galaxy • 835 views
ADD COMMENT • link •
modified 4.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.5 years ago by ghrose • 0

Hello,

We can take a look at your history. Please share a history web link, note which dataset is problematic (if there are several like this), and send the info to galaxy-bugs@bx.psu.edu. Don't post the link here or it will become public.

How to share: https://wiki.galaxyproject.org/Learn/Share

Best, Jen, Galaxy team

ADD REPLY • link written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for Jennifer Hillman Jackson
4.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is an updated post. Thank you for sending in your history. The genome that your sequence mapped to was not in our reference files for this tool (the genome release date was after the reference file creation date). 

We have existing plans to publish a general data update either Fri 6/16 or early the following week. This data will now almost certainly be included. To track progress (and know when the update reference files for this tool are available on usegalaxy.org), please follow this Trello ticket: https://trello.com/c/8ERVQGtX

Thanks for your patience while the root cause of the data discrepancy was investigated. Initial testing indicates that the example hits you shared without taxonomy information now will have it after the update. Actually running the tool with your data in the UI will be the final test - and the results will reflect the most current data available from NCBI. It will be more than is available now and hopefully enough for your analysis.

Best, Jen, Galaxy

   
ADD COMMENT • link modified 4.5 years ago • written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k
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