[mira_talk] Re: Solexa paired-end reads

On Wed, Feb 23, 2011 at 1:17 PM, Tony Travis <a.travis@xxxxxxxxxx> wrote:
>
> Hi, Bastien.
>
> I'm assembling Solexa paired-end reads with MIRA using the default Solexa
> read-naming convention, but I have no idea if MIRA is actually using the
> mate-pair information. I've looked at the logs, but I can't find any
> information about mate-pairs.
>
> I have to admit that I just assumed mate-pair information is used by MIRA.
> However, when I used the "tablet" viewer to examine a MIRA 'ace' file from
> my Solexa paired-end assembly, it showed no mate-pairs.

Hi Tony,

Ace files don't store paired end information explicitly, so Tablet can't show
you anything. I therefore wrote a MIRA assembly format (MAF) to SAM
converter which should then allow you to see the pairs in Tablet (or any
other SAM/BAM viewer): https://github.com/peterjc/maf2sam

I'm happy to have any feedback on the MIRA list.

Peter

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