Question: Fetch taxonomic representation tool error - missing lines
0
gravatar for ibis
3.0 years ago by
ibis0
United Kingdom
ibis0 wrote:

Hello,

I have been using the Fetch taxonomic representation tool from Galaxy online to retrieve taxonomy from NCBI.

I m using tab delimited lists with name - gi number format.

I have noticed that the output randomly skips some lines and doesnt return taxonomy for some of the gi numbers. I have double checked and the data is present on NCBI with the full taxonomy. Also, I ve noticed that in many cases it doesnot return taxonomy for the "larger" most recent gi numbers I have as input.

Any ideas on why this is happening and how to fix it? The output is really good overall but the fact that some entries are missing randomly, means I have to check line by line to find what's missing. :(

Thanks,

ibis

 

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by ibis0
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The source data used by this tool is indexed/updated at the same Megablast databases are updated. On usegalaxy.org, these are older (the exact date can be reviewed on the Megablast tool form).

Updates exist and are pending release to the server. There is no ticket created for this as it is just an internal data update process, but we expect this to be done in the near term.

Our apologies for the current inconvenience, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for ibis
3.0 years ago by
ibis0
United Kingdom
ibis0 wrote:

OK, thanks for the reply Jen!

I hope the updates go through fast because I find this to be a very usefull tool to complement taxonomic assignment steps for OTU data when BLAST falls short for returning the full taxonomy.

Cheers,

Ibis

ADD COMMENTlink written 3.0 years ago by ibis0
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