[mira_talk] Re: Paired end info - SAM/BAM output from MIRA?
- From: "Daniel Depledge" <d.depledge@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 16 Sep 2010 11:31:03 +0100
Hi Bastien,
I would also like to find out about how to convert the Mira output into a
SAM. While such a format is not really required for joining contigs etc it
is very useful for analysing reference mapped sequences in SamTools
(allowing one to look at minority variants etc).
Is there any chance that a Sam output might make it into a later version
of Mira? (I would try it myself but I am not a programmer by any stretch
of the imagination).
Regards
Dan
> On Fri, Jul 2, 2010 at 6:47 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>
> wrote:
>> On Freitag 02 Juli 2010 Peter wrote:
>>> Funnily enough, when I asked the Tablet team if anyone else was
>>> interested in it supporting MAF directly, they also said "Yet another
>>> output format?". Certainly SAM/BAM seems to be the most widely
>>> supported alignment/mapping format for big genome projects, but
>>> I understand that MIRA is more focussed on smaller genomes
>>> where the older file formats suffice.
>>
>> It's not that the "older" file format suffice, it's that they provide
>> the only
>> possibility for MIRA to have the results supported at all.
>
> I would have to agree SAM/BAM are better suited for mapping onto
> existing genomes than for de novo assembly.
>
>>> You mentioned you would like to add tags - the SAM/BAM format
>>> does allow for per-read tags, and I think there is some flexibility
>>> in the header too. I guess it depends on what exactly you need -
>>> I don't see an existing header convention for annotating a region
>>> of a contig.
>>
>> SAM/BAM has no sequencing technology type field, it has no read base
>> tags, no
>> consensus tags no nothing MIRA needs to pass on information about all
>> those
>> things which make life during finishing so easy.
>
> There is a SAM/BAM read group (RG) which might be suitable for
> the technology type (and/or strain information). My impression is
> that all these "optional" tags in the SAM/BAM read tags and headers
> are only minimally defined in the file format specification. The paired
> end stuff is pretty nicely done though (which was what I was initially
> interested in here).
>
> Peter
>
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--
Daniel Depledge PhD
Research Associate
Division of Infection & Immunity
University College London
Windeyer Building
46 Cleveland St
W1T 4JF
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