[mira_talk] Re: Where are my scaffolds?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 24 Aug 2009 20:52:10 +0200
On Donnerstag 20 August 2009 Marcin Swiatek wrote:
> Interestingly, the map alignment algorithm failed to place several fairly
> long pieces with multiple restriction sites. I find it quite puzzling and I
> can't quite figure out what to do with this information. Are these possible
> misassemblies or maybe the pieces are too short, with not enough cuts...?
> Anyhow, this is not really a usage question, I don't even know how to
> phrase it. But if anyone here has a suggestion, that would be greatly
> appreciated.
Hi Marcin,
honestly, I don't know. I never really worked with optical mapping data or
with programs that support it. A quick search turned up SOMA
(http://bioinformatics.oxfordjournals.org/cgi/content/full/24/10/1229) which
looks promising ... did you try that?
Regarding the long pieces that could not be mapped ... misassemblies cannot be
ruled out. You should have a look at these contigs with some dedicated
finishing tools which look at mate-pair coverage etc. whether something turns
up there.
Regards,
Bastien
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