[mira_talk] Re: contigs built only by one sequence
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 10 Jan 2010 22:24:42 +0100
On Sonntag 10 Januar 2010 Laurent Manchon wrote:
> yes i'm agree with you but i have some problems to find the
> corresponding and good command line syntax in the current version
> (mira3rc4d)
> can you help me ?
>
> on v2.9.43 is :
>
> bin/mira -project=planaire -fasta=planaire.fa -job=denovo,est,normal,454
> -OUT:sssip=no -notraceinfo \ -GENERAL:kcim=yes,not=3 -SK:rt=4 \
> -CO:fnicpst=yes,rodirs=10,asir=yes,mr=no \
> -CL:cpat=no,pec=no,pvlc=no,qc=no,bsqc=no,mbc=no,emlc=yes,mlcr=0,smlc=0,emrc
> =yes,mrcr=0,smrc=0 \
> -AL:bip=5,bmin=10,mrs=90:egp=yes:egpl=reject_codongaps:megpp=100,mo=60 \
> -AS:mrl=30,bdq=30 -SK:mnr=yes,rt=8,mmhr=6
Most of the parameter names haven't changed, so they can be re-used quite
easily. But as there are now several technologies fully supported, for many
parameters you need to tell which parameter is for which technology.
In your case it's pretty easy as you have only 454 as technology:
mira -project=planaire
-fasta=planaire.fa
-job=denovo,est,normal,454
COMMON_SETTINGS
-SK:mnr=yes:rt=8:mmhr6
...
454_SETTINGS
-CL:cpat=no:...
...
Try it out. MIRA will tell you if you made an error in the parameter
definition. It's a matter of a couple of minutes.
Regards,
Bastien
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
