[mira_talk] Re: mapping results clarification
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 17 Mar 2010 20:44:47 +0100
On Mittwoch 17 März 2010 Stefano Ghignone wrote:
> Jan
>
> > hm, try accurate instead of normal, this way you do more iterations and
> > maybe some of them will be added later. but if they are in the debris,
> > you are out of luck.
>
> you're right again. Thanks. Accurate mode is much more inclusive...only
> 19 fosmid ends have been put in debris instead of 69 by normal mode.
I suppose that 'accurate' was just a bit more clipping happy.
Anyway: fosmid ends are NOT part of your reference genome. No wonder that MIRA
doesn't like them and discards those ... they have no business being there.
One thing you could try is to screen your sequences with SSAHA2 against your
fosmid vector and use the resulting SSAHA2 file as clipping input to MIRA.
Regards,
Bastien
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