[mira_talk] change stringency in Mira mapping assembly
- From: Christoph Hahn <chrisi.hahni@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Sun, 27 Nov 2011 19:56:52 +0100
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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