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

[Ole K. T. <o.k...@bi...>]

Hi Heiner,
I have another 454 8 kb library and an Illumina 5 kb library (plus a 3
kb 454 library).  I'm really interested in hearing your workaround.

Ole

On 19 July 2012 13:31, kuhl <ku...@mo...> wrote:
> 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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