Re: [AMOS-help] clousure gaps

[Michael S. <mic...@gm...>]

Hi Alex,

Unfortunately we do not have any automated tools for this. It may be
possible to correct this by adjusting some of the parameters of the
assembler (especially the astat cutoffs), but there is no automated
way to correct for it. What organism is it? Maybe we could collaborate
on it.

Good luck!

Michael Schatz




On Sat, Jul 18, 2009 at 1:38 PM, Alex Di Genova<dig...@gm...> wrote:
> Hello all:
>
> I make an assembly and assebly validation process using celera
> asssembler and amosvalidation pipeline. Looking the linkig report in
> hawkeye I see very links that the scaffolder nontake into account. So
> several of this linking contig allowing to me for clousure certain
> gaps in the current assembly, The questions is AMOS package have some
> tool for clousure o locate this linked contig into the scaffolds.
>
> thank in advance
>
>
>
>
>
>
> Alex Di Génova.
> Ingeniero en Bioinformatica.
> Laboratorio de Bioinformatica y Matemática del Genoma.
> Centro de Modelamiento Matemático.
> Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile.
> Avenida Blanco Encalada 2120, Piso 6.
>
>
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