[mira_talk] Re: some questions

On Mittwoch 06 Mai 2009 Laurent MANCHON wrote:
> thank you so much for this help Bastien,
> just a question:
> Do you see something wrong or not good in my command line below:
>
> mira -project=ESTUR -job=denovo,est,normal,454 -SK:mnr=yes -SK:rt=4
> -GE:not=2 -CO:asir=yes -CO:mr 454_SETTINGS
> -AL:mrs=95:egp=yes:egpl=reject_codongaps:megpp=100 -CO:rodirs=10
> -AL:mo=60 -CL:cpat

The definition of "wrong" depends entirely on your goals. You have a mixture of 
lenient and less lenient alignment parameters.

-CO:asir=yes will lead to "clustering" of close sequences, even if they'd 
"really" differ in vivo.

-AL:mrs=95 is a very strict parameter, as is the combination -
AL:egp=yes:egpl=reject_codongaps:megpp=100

-CO:rodirs=10 agian relaxes things a bit.

I'd say that this command line leads to mixture of "true EST sequences" and 
some "clustering-like sequences". But that's just a guess.

Regards,
  Bastien


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