[mira_talk] Re: hybrid assembly question
- From: 周琦 <zhq_kiz@xxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 7 Jul 2009 23:19:27 +0000
Hi,Bastien:
I produced 130Mb scaffolds from Solexa reads with SOAPdenovo, the longest
scaffold is about 1Mb. I used unaltered contigs/scaffolds without shreding
them. The organism genome size is about 200Mb. Thank you.
> From: bach@xxxxxxxxxxxx
> To: mira_talk@xxxxxxxxxxxxx
> Subject: [mira_talk] Re: hybrid assembly question
> Date: Wed, 8 Jul 2009 01:08:09 +0200
>
> 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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