[mira_talk] Re: Help with MCVc (missing Co Verage in consenus) after mapping assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 4 Feb 2014 20:34:46 +0100
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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