[mira_talk] Re: How does MIRA use paired end information?

eek... you baffled me with bull... as the saying goes.

I'll read through these links and get back to you if they don't clear things
up for me.

Thanks Bastien!

On Thu, Sep 15, 2011 at 3:13 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

> On Sep 15, 2011, at 23:54 , Evan wrote:
> > So if MIRA has further passes to preform before it completes will it scan
> through each contig and check for read pairs that are:
> [...]
> > And correct any inconsistencies by removing these reads from the contig
> and placing them back into the pile of unassembled data?
>
> Will you be very disappointed if I tell you hat for each pass, MIRA places
> back *all* reads into the pile of unassembled data? :-)
>
> And yet it gets most repeats disentangled that way. Before I try to tell
> you it's simply magic: you might want to have a look at the thesis (
> http://chevreux.org/mira_papersnposters.html and there pages 32 and 81++),
> the article I have on miraEST in Genome Research (
> http://genome.cshlp.org/content/14/6/1147.full.pdf+html) as well as a
> couple of sections in the manual:
>
>
> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_intro_miradiscernsrepeats
> and
>
> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_snp_discovery
> and
>
> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_tags_set_and_used
>
> B.
>
>
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