[mira_talk] Re: After Scaffolding
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 18 Sep 2009 22:43:47 +0200
On Donnerstag 17 September 2009 Davide Sassera wrote:
> [...]
> I did see some with the assembly with nrr 10, but now with the assembly
> with nrr 7 I don't see any (for now).
> I don't know if the nrr parameter and the way chimeras are assembled are
> anyhow related, but well, now the assembly seems ok.
Strange.
> the pipeline mira --> Bambus --> mira seems to work, but what parameters
> would you use for the mapping assembly on the bambus backbone? I used
>
> # mira -project=1709 -job=mapping,accurate,454,genome
> -SB:sbuip=0:abnc=no -SK:mnr=yes:nrr=7
> sounds good?
In mapping assemblies, -SK:mnr:nrr should not be necessary. Try it without.
> on the other hand the pipeline
>
> mira --> gap4 to tweak, correct and merge --> bambus --> mira
>
> does not work. The problem is that Bambus does not like the ace file
> generated with gap2caf.
> Any ideas?
Yes :-)
gap2caf produces, as the name suggests, a CAF file and not an ACE file. Put
the CAF through "convert_project -f caf -t ace ..." to use the resulting ACE
with bambus.
Regards,
Bastien
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