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

[Walenz, B. <bw...@jc...>]

Hi, Ole-

We tried this on a plant genome for the exact same issue, with little
success.  The 3kb mates spanned repeats that classifyMates was unable to
search through, resulting in either enormous compute times.

If you want to try it, the latest in CVS, I think, allows innie again.  Be
sure to use -nosuspicious.  If not, flipping the reads works too.

Use the 'random path' search -rfs.   Instead of exhaustively searching, this
will follow N random paths through the overlap graph.

b


On 7/18/12 5:02 AM, "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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