[mira_talk] Re: Paired end info - SAM/BAM output from MIRA?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 19 Sep 2010 19:12:51 +0200
On Freitag 17 September 2010 Peter wrote:
> I managed to hack together a MAF to SAM script in Python,
Hey, that would be a nice thing to make available :-)
> 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...
Indeed. For "paired-end only", this is the way to go ... it could even be
straight-forward if SAM works as I think it works.
For Sanger-type, one-DNA-template-may-have-more-than-two-reads finishing reads
however things won't work at all: SAM/BAM does not support this kind of data.
But as I wrote, a script that converts the "simple" cases would also be
welcome :-)
B.
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