[mira_talk] Re: Paired end info - SAM/BAM output from MIRA?

  • From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 17 Sep 2010 12:22:05 +0100

On Thu, Sep 16, 2010 at 8:12 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> On Donnerstag 16 September 2010 Daniel Depledge wrote:
>> I would also like to find out about how to convert the Mira output into a
>> SAM.
>
> I currently know none, sorry. SAM is on my TODO, but pretty low at the moment.
>
> B.

I managed to hack together a MAF to SAM script in Python, but there was
one thing which would needed work: representation of any paired reads in
the MAF file. I had fallen back on looking at the read names (but of course
MIRA supports multiple different naming conventions). I think I should be
using the DI and TN information here...

Peter

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