[mira_talk] Re: After Scaffolding
- From: Davide Sassera <davide.sassera@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 17 Sep 2009 14:00:04 +0200
Bastien Chevreux wrote:
On Freitag 11 September 2009 Davide Sassera wrote:
1 Repeats: could you please tell me what nnr would you set in this
situation?
If MIRA does not complain (MEGAHUBS and such), none. If it complains: try 20.
If still complaining: 15, 10, 9, 8, 7, ...
I tried some and in the end it seems that switching nrr to 7 changes
things.
The assembly with 7 seems good
Why do you want to tweak? Do you have the impressions that there are still
chimeras?
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.
I'm also working with Bambus and I have a couple of questions:
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?
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?
thanks
D.
--
Davide Sassera
Sezione di Patologia Generale e Parassitologia
Dipartimento di Patologia Animale,
Igiene e Sanita` Pubblica Veterinaria
Facolta` di Veterinaria
Universita` degli Studi di Milano
Via Celoria 10, 20133, Milano, ITALY
Tel: +39 0250318094
Fax: +39 0250318095
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