[mira_talk] mapping assembly - decrease number of allowed missmatches

Hi MIRA experts,
I am using MIRA to do mapping assemblies of mitochondrial genomes of parasitic flatworms using the known mitochondrial genome as reference. It works nicely - in most cases.. Some of my libraries are unfortunately contaminated with a second flatworm species (the libraries were produced from 100 pooled individuals, that were all picked from the same host, but it seems as if some host were infected with more than one species), so in this cases the mapping assembly results in a kind of chimeric mt genome, where conserved regions get hits from both species.
I confirmed the two species by separately mapping the reads onto the two mt genomes (using Novoalign) with allowing only one missmatch (the species are substantially different, expect for the conserved regions). Then I just used the reads that mapped and did denovo assembly which resulted in clean parts of the mt genome of one of the two species, respectively.
I would like to use the same approach for the MIRA mapping assembly, so my questions are:
-Is it possible to decrease the number of allowed missmatches to, lets say, allowing only one missmatch? I was thinking about using the "min_relative_score(mrs)" option. My reads are 100bp so setting "-AL:mrs=99", should do what I want, right? As far as I understand I d have to set [-SK:pr] to 99 then also, right?
-Is it possible to feed Mira with two or more separate mt genome "reference strains" within one mapping assembly? 

Thanks for your help!

Much obliged,
Christoph

--
You have received this mail because you are subscribed to the mira_talk mailing 
list. For information on how to subscribe or unsubscribe, please visit 
http://www.chevreux.org/mira_mailinglists.html

Other related posts: