Thanks Peter,

Excellent point. From there, the "Cut" tool could be used to reorganize the output to exactly match that of the 13-column regular megablast output. So, no external data needed, no tool modifications needed.

This can't be done on the main public Galaxy instance as BLAST+ is not available there, but for any local/cloud instance this is an alternative certainly work testing.

Best,

Jen
Galaxy team

On 4/24/12 2:36 PM, Peter Cock wrote:
On Tue, Apr 24, 2012 at 10:24 PM, Jennifer Jackson<j...@bx.psu.edu>  wrote:

..., using
the BLAST+ BLASTN megablast wrapper that Peter authored, in a local or cloud
instance, would be the best immediate remedy (this version has the standard
12 column output). Sequence length data could always be obtained from
Genbank and added into these results using other Galaxy tools (column join,
etc.).

Getting the query and match sequence lengths is even simpler that
that with the BLAST+ wrappers - just select the "extended" tabular output.
Of course, you'll need to adjust the downstream analysis to take into
account the different column numbers.

Peter

--
Jennifer Jackson
http://galaxyproject.org
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