Galaxy Megablast Output

Question

[zgayk]

Hello,

I have been playing around with the bioinformatics tool Galaxy and am specifically trying to interpret the Galaxy megablast output. What I am really interested in is whether the Query Seq-id column can be displayed in Galaxy as the gene or sequence name it is matching to from NCBI? Or is the the only way to find out what the sequence is to search this number in NCBI and see what the name of the gene is?

Thank you very much,
Zach

Answer 1

[Aerval]

There are probably better ways, but you could use blast_reporting to transfer your report in a 24-column tabular file and then look in column 20-something for the definition/description

[zgayk]

Thank you very much for the advice. Are there any good tutorials on how to install a tool from the Galaxy tool shed? I found blast_reporting, but all of the tutorials mention being a galaxy administrator to install from the tool shed into galaxy and I am not. I have not been able to install blast_reporting even though I can find it. Thank you,

Zach

[Aerval]

Sorry, I did not see your response. Anyways, if you are still into the problem, I fear I can not help you as it sounds as if you are on a third party server and can not install tools there. You would need to have an own galaxy server running (you could have that on your pc in the background, though it will be some work) or know someone from your server to be able to install tools for you. So yeah, with out being admin my answer does not help you :(

[zgayk]

Thanks very much. I did not see your response, but am considering creating my own galaxy admin account. Thanks again.

Zach