Bastien Chevreux a écrit :
On Donnerstag 04 März 2010 Alexie Papanicolaou wrote:my two cents: One option would be to map your reads to the reference consensus (created by MIRA) using a program like maq/bowtie (one strain at a time).I think the problem was she doesn't have them separated, but rather as a mixture.
exactly!I went for the -CO:msr=no and it ran well (I had teras of disk available... was not an issue).
Now, I'll point at my variants! Thanks for this kind help, Fleur
I don't know about maq/bowtie, but I think they don't handle large discrepancies (inserts / deletions) more than a couple of bases very well. With MIRA you might get those and even if not, it will set a whole armada of tags pointing to that problematic site.Regards, Bastien
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