[mira_talk] Re: hybrid assembly question

On Dienstag 07 Juli 2009 周琦 wrote:
> Hi, glad to have mira and the discussion forum here.  I'm a new guy to
> mira, so not sure I did it right:
> [...]
> mira -GE:not=8 -fasta -project=hybrid -job=denovo,genome,normal,sanger,454
> -notraceinfo

Hello Qi,

one first thing: I think you should tell MIRA not to clip the "sanger" reads: 
"--noclipping=sanger"

But could you give some more info on what you did? I'm not sure I understand 
what you mean with "130Mb assembled scaffolds produced by Solexa". Did you take 
unaltered contigs? If yes, did you shred the longer ones (>20kb)? How big is 
the organism you try to assemble?

Regards,
  Bastien


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