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

[Sharon Wei]

I ran into the same problem before and from my experience, the only 
solution is to use dummy scaffolds, otherwise the ensembl API won't work 
correctly.

Sharon

On 8/31/12 12:20 PM, Dan Bolser wrote:
> 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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