Re: [wgs-assembler-users] Bimodal mate pair library, can I use denovo classification?

[kuhl <ku...@mo...>]

Hi Ole,

what other kind of large insert libraries do you have? I might have a
suitable workaround for such problems.

Best wishes,

Heiner



On Wed, 18 Jul 2012 11:02:56 +0200, Ole Kristian Tørresen
<o.k...@bi...> wrote:
> Hi,
> I have a bimodal mate pair library with one peak around 3kbp and the
> largest and real peak at 19kbp. When I include this in the assembly,
> the scaffolding take ages and the result is not that good (larger than
> biological probable scaffolds). If I don't include it, scaffold is
> quite quick, but the assembly is a bit more fragmented that with it
> included. Without I get around 20000 scaffolds, and I get 7000
> scaffolds with it included (around 7000 with Newbler too, which
> handles this kinds of library better than CA I think). So I would
> rather like to include the library.
> 
> classifyMates does not seem to be able to find innie oriented mates,
> only outtie PE mates as far as I can see. Could I get around this in a
> way? Pretend that the library is outtie, and search for outtie mates
> with seperation up to 5kbp or something?
> 
> Thank you.
> 
> Ole
> 
>
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