Hi Sarah,

Peter defined the columns (thanks) but I can provide some information about the GenBank identifiers. The megablast database on the public server are roughly a year old and there have been updates at NCBI since that time. As I understand it, this manifests as occasional mismatches between hits at Galaxy vs Genbank when comparing certain IDs linked to updated records.

We are working to update these three databases, but there are some complicating factors around this processing specifically related to the public instance and the metagenomics workflow that have yet to be resolved. Please know that getting updated is a priority for us and we apologize for the inconvenience.

To use the most current databases, a local or (better) cloud instance with either the regular or BLAST+ version of the tool and a database your choice is the recommendation. Instructions to get started are at:
getgalaxy.org
getgalaxy.org/cloud

Hopefully this explains the data mismatch. This question has come up before, but I think you are correct in that the final conclusion never was posted back to the galaxy-user list (for different reasons). So, thank you for asking so we that could send out a clear reply for everyone using the tool.

Best,

Jen
Galaxy team

On 4/23/12 9:56 AM, Sarah Hicks wrote:
I am having trouble finding information on the MegaBLAST output
columns. What is each column for? I can't seem to figure this out by
comparing info in the columns to NCBI directly because the GI#'s don't
match with the correct entry on NCBI. I've seen that others have
posted about that problem, so I'm also waiting on details on that
question, but for now, I'd just like to know what to make of the
output...
best,
Sarah
___________________________________________________________
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
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

--
Jennifer 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
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to