[mira_talk] Re: MIRA 3.0.5 error from Assembly::extendADS
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 23 Apr 2010 17:04:48 +0100
On Thu, Apr 22, 2010 at 7:56 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> On Donnerstag 22 April 2010 Peter wrote:
> > What files would help to diagnose this? The reads themselves zip up to
> > about 3.5MB so potentially I could send you them off list (it is
> > unpublished data).
>
> Damn, I thought this bug was dead.
>
> Reads off list please. Pretty busy at the moment, I'll put those in the
> backlog for when I have an hour or two to spend on it.
OK.
> > If you think it could make a difference, I can try this on a Linux
> > machine tomorrow - currently I'm using MIRA on Mac OS X.
>
> Won't make a difference. Switch off read extension will do the trick here:
> "-DP:ure=no" for Sanger (and 454 for good measure).
That worked (the assembly finished), thanks :)
I think I need to explore all the MIRA trim options here - I'd been
manually trimming my 454 to remove both the MID barcode and
our PCR primer sequence (otherwise I was finding MIRA would
extend the reads back into the primer).
Peter
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