[mira_talk] Re: change stringency in Mira mapping assembly

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 28 Nov 2011 22:15:45 +0100

On Nov 28, 2011, at 21:32 , Christoph Hahn wrote:
> One more question concerning mirabait: Say you know that your data contains 
> contaminations with host DNA in addition to the parasite data you are 
> interested in, I suppose mirabait could be used also to find this 
> contaminations in the illumina data set, right? One would just need a decent 
> reference or "bait" dataset from the host organism.. Any potential problems 
> with this approach?

No, I use this kind of approach for a couple of tasks. As long as the reference 
is sufficiently close and there is no common sequence shared between host & 
parasite, things work as expected.

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