[mira_talk] Re: Paired end info - SAM/BAM output from MIRA?
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 2 Jul 2010 10:35:34 +0100
On Thu, Jul 1, 2010 at 7:32 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> On Donnerstag 01 Juli 2010 Peter wrote:
>> I'm starting to get more paired end data, and would like to be able look
>> at this information in alignment viewers. What MIRA output file format
>> would you recommend for this?
>
> At present I use CAF and caf2gap to convert to a gap4 database.
Do you like gap5?
I'll have to have another attempt at installing gap4 or gap5 on my Mac...
>> [...]
>> Bastien - Is SAM (or even BAM) output something you are thinking
>> about supporting directly in MIRA?
>
> Yet another output format? :-)
>
> It's not been requested so far. At first sight I miss the possibility to add
> important things like tags, which greatly reduces the usefulness of that
> format.
>
> I don't say I'll never implement that format, but it won't happen soon.
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.
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.
Peter
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