No conflicts on my end. Actually, it would be a rather convenient
(and accurate) annotation to refer to the aligned species by region.
On Aug 24, 2006, at 5:39 PM, James Taylor wrote:
The problem here is that there are multiple sequences with the name
'baboon.1'. In fact, in the ENCODE TBA alignments there is a
different 'baboon.1' for every ENCODE region, so when you concatenate
MAFs across multiple regions you get a result that GMAJ (rightly)
To correct this I think the only thing we can do is change the MAFs
provided by the encode group so that every orthologous sequence has a
unique name across encode regions. So baboon.1 -> baboon.ENm001_1,
and so on.
All, would such a change break any existing tools / analysis?
On Aug 24, 2006, at 5:20 PM, Ross Hardison wrote:
> I'm trying to use the GMAJ tool on Galaxy, but get this error:
> Error loading alignments from bundled file "input.maf":
> edu.psu.bx.gmaj.BadInputExceptions: Sequence length contradiction"
> s baboon.1 26891 63 + 1248010
> Current = 1248010. Previous = 550206
> The maf files were extracted using the "Extract MAF blocks" tool, for
> TBA ENCODE alignments.
> The maf data are at
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