[ensembl-dev] Multiple 'paths' in assembly table?

Dan Bolser dbolser at ebi.ac.uk
Fri Aug 31 17:20:08 BST 2012


Hi,

Some of my contigs map to chromosomes via scaffolds, and some are
included in chromosomes directly. This means that there are multiple
(two) paths from contig to chromosome. No matter what I put in meta
(assembly.mapping), it seems I can't project both types of 'seqlevel'
to 'toplevel' correctly.

Either I can project only those contigs found in chromosomes via
scaffolds OR only those contigs found in chromosomes directly, but not
both types with one set of assembly.mapping meta keys.

Is it possible to correctly project either type of contig with one set
of assembly.mapping meta keys?

I need this to correctly run the 'set_toplevel.pl' script.

I can get round the problem by adding dummy scaffolds for all my
contigs that are not part of real scaffolds, but this introduces
thousands of dummy seq_regions and assembly entries... Obviously, if
this is the only way to do it, that's what I'll do.

Finally, how much time does the assembly.mapping meta key save?
Thinking about it, I can't convince myself that you save any extra
queries by having this information (but I haven't looked at places in
the API where it may be used).


Thanks for suggestions,
Dan.




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