[mira_talk] Re: Help with MCVc (missing Co Verage in consenus) after mapping assembly
- From: Austen Chen <cyausten@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 5 Feb 2014 13:18:24 +1030
Thank you so much everyone for your help and suggestions and i will give
them a go and then let you know.....
Cheers
Austen
On Wed, Feb 5, 2014 at 6:04 AM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On 04 Feb 2014, at 14:22 , Austen Chen <cyausten@xxxxxxxxx> wrote:
>
> [...]
> Presumably A1 and A3 would have a common missing region from
> 165410-165814, but this is not the case as each missing position in A1 and
> A3 is not referring to the same position in relation to the reference
> sequence, and hope i have explained it here clearly. it looks like i am
> able to find missing coverage in each strain but unable to find common
> missing coverage between these 2 strains, and that's why I was asking you
> for help if my interpretation was correct and you could give me some
> suggestions on how to tackle this problem.
>
>
> As I wrote: convert the gap4 database (with your edits) back to CAF, then
> use "miraconvert -t cstats" to recreate some standard info files of MIRA,
> but using that new CAF file. You should get a new info file about consensus
> tags, which contains also the MCVc tags, have a look at that file. Though
> I'm not sure whether these positions would be really wrt to the reference,
> I need to check.
>
> Anyway, converting to SAM *should" give you positions which are based on
> the reference (there is no other way), you'd just need to parse out the
> tags out of the SAM.
>
> HTH,
> B.
>
>
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