On Sat, May 7, 2011 at 12:01 AM, Douglas Rhoads <drho...@uark.edu> wrote:
> We have a local install of Galaxy and are using it for training grad and
> undergrad students (using the Windshield Splatter data).  We have a
> relatively new install and the Megablast seems to be doing something funny
> with the output in that column 2 which is supposed to be the GI of the
> database hit is now two numbers joined with an underline (see below).  I
> need to tell my IT people what is wrong so they can correct the problem.
> BL1-1-3     157649053_111750     91.30        46             4              0              10             55             58541       58496       2e-
> 06             60.0
> BL1-1-5     161788633_175843     100.00       26             0              0              15             40             48812       48787       4e-
> 04             52.0

Which version of BLAST do you have?

If you're using the "megablast" tool in Galaxy, then it will be NCBI
"legacy" BLAST using the blastall binary.

If you're using the (commented out by default) BLAST+ wrappers, then
it will be using the blastn binary. There were changes to the ID
handling in the tabular output in BLAST 2.2.25+ as I recall.

Another important factor is how the BLAST database was made (with or
without the -parse_seqids flag).


P.S. Questions like this about local installs might be better on the
galaxy-dev list, CC'd.

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