[mira_talk] Re: Paired end info - SAM/BAM output from MIRA?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 2 Jul 2010 19:47:11 +0200
On Freitag 02 Juli 2010 Peter wrote:
> 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 didn't even try it out *cough* gap4 works out pretty well until now. But I
think I need to give gap5 a try 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.
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.
> 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.
B.
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