[mira_talk] Re: TGICL and Mira

On Wednesday 26 November 2008 09:40, Laurent MANCHON wrote:
>[...]
> Okay thank you for this help.
> So just one thing, in TGICL i have used those parameters :-l 60 -v 20
> (with l : miminum overlap length (default 30) and v : maximum length of
> unmatched overhangs (default 30)) what are the corresponding parameters i
> have to use in MIRA ?

Use "-AL:mo" for emulating the '-l', so if you have both Sanger and 454 
sequences, the command line would be: 
    mira ... -AL:mo=60 454_SETTINGS -AL:mo=60

The '-v' I don't think I have something similar. You can emulate this through 
with "-AL:mrs". Depending on the length of your sequences, use values between 
80 (454GS20 sequences) and 95 (454 Titanium and Sanger sequences).

Regards,
  Bastien

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