[mira_talk] change stringency in Mira mapping assembly

Hi Mira-people!

In order to assemble a mitochondrial genome I want to perform a Mira mapping assembly and use the reference mitochondrial genome of a related species to "extract" mitochondrial reads from my illumina lane.

I did the following (inspired by the very helpful documentation on http://mira-assembler.sourceforge.net/docs/chap_solexa_part.html):

mira --project=salarismtlane8 --job=mapping,genome,accurate,solexa -AS:nop=1 -SB:bsn=salaris_mt:bft=gbf:bbq=30 SOLEXA_SETTINGS -CO:msr=no -GE:uti=no:tismin=120:tismax=200 -SB:dsn=salarismtlane8

Actually it worked nicely, but my problem is that there are still lots of gaps and the mt genome is far from complete. As the reference is not closely related I think I would need to allow more missmatches in the mapping assembly. Is there an easy way of doing this? Maybe by not just using the standard SOLEXA_SETTINGS?

Can anyone please give me a hint?

Much obliged!
Christoph




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