[mira_talk] Re: Paired end info - SAM/BAM output from MIRA?
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 20 Sep 2010 10:44:54 +0100
On Sun, Sep 19, 2010 at 6:12 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> 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.
I will investigate...
> 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.
No, but there has been discussion about this on the samtools-devel
mailing list. Are you subscribed? This functionality will also be needed
for PacBio strobe reads.
> But as I wrote, a script that converts the "simple" cases would also be
> welcome :-)
I guess in the long term direct support in MIRA (e.g. convert_project)
would be ideal, but a Python script would suffice in the short term.
I do plan to release this once the paired end stuff works.
Peter
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