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.

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