[mira_talk] Re: MappingAssemblyIontorrent
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 30 Jun 2013 15:10:40 +0200
On 06/26/2013 11:47 PM, Martin Mokrejs wrote:
So why mira could not run by default in a mode that it would use
"mapping" for the speedup of work but present only assembled reads of
the sequenced strain, NOT the chimera between my strain and the
reference strain. If that is what you are talking about here. ;-)
Producing the chimera should have never happened in my eyes, maybe
except if the file prefix would have been altered then people might be
pleased to get that as an additional bonus. ;
Well, my initial use case for the mapping functionality of MIRA was
indeed to reconstruct one genome from sequencing data of two slightly
different (and horribly undercovered) strains. Afterwards, almost the
same game with early Solexa data: full reconstruction of a genome where
I had the reference but not really well covered by Solexa data. So,
having MIRA give me the chimeric reconstruction made more than sense to me.
But times have changed: one more often than not has now too much data
and seeing that other users have problems, I changed the default behaviour.
So where is the chimera hiding now in 3.9.x series? ;-)
The default FASTA output on mapping is now the same as when converting
the result MAF to FASTA: you'll get one FASTA file per strain, and one
additional file (conveniently called "AllStrains") for the merged data.
B.
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