[mira_talk] closing sequence assembly

Hi Bastien,

I have a different type of problem here. Now I have a draft assembly and a 
bunch of BACs assembled  manually to the draft assembly. The result is in the 
form of --(contig1)---><--BAC--- ---(Contig2)---> format where there are 
certain amounts of mismatches and gaps in between. Although I know the 
orientation etc. I actually don't want to join them manually. Instead I would 
like to run an assembly of the said BAC and the 2-3 contigs that I know can be 
joined together. Can I use MIRA for this?

Thanks

Sucheta
----- "Bastien Chevreux" <bach@xxxxxxxxxxxx> wrote:

> On Thursday 30 April 2009 Sucheta Tripathy wrote:
> > As I reported last time, the assembly output was not OK, with very
> shorter
> > fragments and the total assembled data much less than expected. Is
> there
> > any other parameter setting I can try to get a better result?
> 
> Ouch, sorry to have forgotten you. I think you've been hit by a bug in
> 
> 2.9.44x2: 
> - bugfix: setting -SK:mchr to values >4095 led to am integer overflow
> and
>   subsequent poor assemblies ... or no assembly at all
> 
> (I think you used a larger value for -SK:mchr)
> 
> You could:
> - try 2.9.44x2 with -SK:mchr=4095
> - try 44x3
> - or wait for a couple of minutes while I am preparing 44x4 which
> fixes another
>   bug (recognition of chimeras).
> 
> Regards,
>   Bastien
> 
> 
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