Hi, Can you please tell me how to work with viral metagenomics in Galaxy? When uploading the data files, there is an option to select the reference genome but in case of viral metagenomics, I can't select any individual genome. What will I do in this step? After uploading and processing the data, I will have to BLAST all my sequences using NCBI BLAST but there is no BLAST option in galaxy. How can I do that? And, is there any way to change the default E-value of Galaxy? Thanks, Mohiuddin
On Mon, Feb 25, 2013 at 5:09 PM, Mohammad Mohiuddin wrote:
Hi,
... After uploading and processing the data, I will have to BLAST all my sequences using NCBI BLAST but there is no BLAST option in galaxy. How can I do that? And, is there any way to change the default E-value of Galaxy?
Hi Mohiuddin, The public Galaxy server only offers Megablast (under NGS:Mapping) and only against four specific databases. If you want more options, there are wrappers for the NCBI BLAST+ suite in the Galaxy Tool Shed http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus which can be installed in a local copy of Galaxy. If your group, department/university/company has their own Galaxy Instance, speak to your local Galaxy administrator about this. Regards, Peter
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Mohammad Mohiuddin -
Peter Cock